[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"        "-oTKIRP-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/KIRP-TP/10005964/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/10013758/transformed.cor.cli.txt"

nPatients in clinical file=202, in cluster file=224, common to both=198
[1] "Reduce the number of clustering variables from 80 to 69."
[1]  69 198
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6               192 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6               192 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               15               183 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               15               183 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               37               161 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               37               161 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               39               159 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               39               159 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               58               140 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               58               140 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               68               130 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               68               130 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6               192 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6               192 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               193 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               193 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               27               171 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               27               171 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               27               171 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               27               171 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                8               190 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                8               190 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6               192 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6               192 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              120                78 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              120                78 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              121                77 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              121                77 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12               186 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12               186 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               17               181 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               17               181 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               195 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               195 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                190 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                190 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                190 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                190 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                10                188 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                10                188 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 9                189 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 9                189 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                81                117 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                81                117 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                81                117 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                81                117 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                22                176 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                22                176 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                195 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                195 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                193 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                193 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               106                 92 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               106                 92 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               102                 96 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               102                 96 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               120                 78 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               120                 78 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               135                 63 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               135                 63 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 9                189 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 9                189 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                192 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                192 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                194 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                194 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                194 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                194 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                69                129 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                69                129 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                71                127 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                71                127 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                12                186 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                12                186 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               67               131 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               67               131 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               20               178 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               20               178 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               13               185 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               13               185 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               15               183 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               15               183 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               194 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               194 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               19               179 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               19               179 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               20               178 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               20               178 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               191 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               191 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7               191 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7               191 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               15               183 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               15               183 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               18               180 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               18               180 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10               188 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10               188 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5               193 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5               193 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               25               173 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               25               173 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               26               172 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               26               172 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                12                186 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                12                186 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                12                186 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                12                186 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                12                186 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                12                186 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                15                183 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                15                183 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                178 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                178 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                36                162 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                36                162 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                21                177 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                21                177 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                194 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                194 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 6                192 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 6                192 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 9                189 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 9                189 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                32                166 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                32                166 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                33                165 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                33                165 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                13                185 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                13                185 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                186 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                186 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                32                166 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                32                166 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                47                151 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                47                151 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               20               178 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               20               178 
[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] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 198 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
         554           21          493            3           NA           NA 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
         582           27           NA            7           49            2 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
         140          780          729           NA          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
         597          600          436          379          516           NA 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-A4-A772 
          NA            2          118           87            4           NA 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
          NA         1778         1636          412          923          763 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
        1357           26           67          595          223          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
         747          108          510           14         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379           85         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
         671           64          585          207            5          102 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
         167           52         2639          586          270         1938 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
          NA           NA         1454           NA         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
         921          792          771          403           NA          233 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
          29          364           NA           84         3760           NA 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        2948         2839           NA         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
         799          612           NA          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         116          353          414         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        2429         2460           NA         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
         578          757           97           10            7           36 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
         208         1575         1479           NA         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 
         765          446          786          279           NA         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          178           91 
TCGA-HE-7128 TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          NA           NA           NA         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        1726          167          511          608           62          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD 
         649          146            2           NA            4          160 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          391          543          438 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         292           11          541          148         3035         2653 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
          NA           NA         2584         2816          391          174 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
          57         1079         1199          994          508          423 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS 
          NA          102          925           NA          494         1247 
TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         847          224            2          186          181          205 
Variable 1:'AGE':	nDistinctValues=51,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=161,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
 [3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
 [5] "PATHOLOGY.M.STAGE"           "GENDER"                     
 [7] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
 [9] "RACE"                        "ETHNICITY"                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 198 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=51, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
130  18  48   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  130    18    50 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
130  18  48   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  130    18    50 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
33 20  4 
[1] "table(vv)"
vv
N0 N1 N2 
33 20  4 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
33 20  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
33 20  4 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=15, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED     3   1
  1P GAIN WILD-TYPE 163   6
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4               169 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                 6 
$`1P GAIN MUTATED`
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-GL-7966 TCGA-IA-A40Y 
          87           26          112           62 

$`1P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
         516            2          118            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
         412          923          763         1357           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
           5          102          167           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         792          771          403          233           29          364 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
          84         3760         2948         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1516          799          612          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         116          353          414         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        2429         2460         1856         1670         1040          578 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 
         757           97           10            7           36          208 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
        1575         1479         1194         1059          765          446 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
         786          279         1967         5925          393          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          32          178           91         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 
        1726          167          511          608          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         146            2            4          160          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          391          543          438          292           11 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         541          148         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
         391          174           57         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         508          423         1973          102          925          494 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
        1247          847          224            2          186          181 
TCGA-Y8-A8RZ 
         205 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               26                 2 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              112              5925 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             74.5             511.0 
[1] "26.0 - 112.0 (74.5)"  "2.0 - 5925.0 (511.0)"
[1] "hr=" "99" 
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P GAIN MUTATED         0        0         5        1
  1P GAIN WILD-TYPE     122       11        37       11
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 0               122
  STAGE II                0                11
  STAGE III               5                37
  STAGE IV                1                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                 T1  T2 T3+T4
  1P GAIN MUTATED     1   0     5
  1P GAIN WILD-TYPE 129  18    45
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1                  1               129
  T2                  0                18
  T3+T4               5                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"
                   vv
clus                N0 N1 N2
  1P GAIN MUTATED    0  4  0
  1P GAIN WILD-TYPE 33 16  4
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0               0                33
  N1               4                16
  N2               0                 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 MX
  1P GAIN MUTATED    1  1  4
  1P GAIN WILD-TYPE 80  7 92
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               1                80
  M1               1                 7
  MX               4                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     4   2
  1P GAIN WILD-TYPE  54 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4    2
  1P GAIN WILD-TYPE   54  138
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               4                54
  MALE                 2               138
[1] 2 2
[1] FALSE
D1V8, continuous
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                51 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8310        TCGA-A4-8311 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A4-8312        TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A4ZT 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G7-7502        TCGA-G7-A4TM        TCGA-G7-A8LD        TCGA-IA-A40U 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IA-A40X        TCGA-J7-8537        TCGA-Q2-A5QZ        TCGA-SX-A71R 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SN        TCGA-SX-A7SO        TCGA-SX-A7SP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A7SQ        TCGA-SX-A7SS        TCGA-SX-A7SU 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     0
  1P GAIN WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           0     5
  1P GAIN WILD-TYPE                        49   124
D1V10, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      0                49
  WHITE                                          5               124
[1] 4 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, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0   5
  1P GAIN WILD-TYPE   9 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    5
  1P GAIN WILD-TYPE    9  148
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               5               148
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED     9   3
  1Q GAIN WILD-TYPE 157   4
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               12               161 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                3                 4 
$`1Q GAIN MUTATED`
TCGA-A4-7287 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 
          21           87           26          921          771          233 
TCGA-BQ-5891 TCGA-G7-6789 TCGA-G7-A8LD TCGA-GL-7966 TCGA-IA-A40Y TCGA-Q2-A5QZ 
          29          208         1967          112           62           57 

$`1Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
           2          118            4         1778         1636          412 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
         923          763         1357           67          595          223 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         659          747          108          510           14         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
         307          930         1049          379           85         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
         857          803          627           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1338          671           64          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         102          167           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5888 
        1938         1454         1242          792          792          403 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
         364           84         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1533         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         218          116          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
         578          757           97           10            7           36 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
        1575         1479         1194         1059          765          446 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
         786          279         5925          393          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         167          511          608          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
           2            4          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
         174         1079         1199          994          508          423 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU 
        1973          102          925          494         1247          847 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         224            2          186          181          205 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               21                 2 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             1967              5925 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             99.5             516.0 
[1] "21.0 - 1967.0 (99.5)" "2.0 - 5925.0 (516.0)"
[1] "hr=" "22" 
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED         1        0        11        3
  1Q GAIN WILD-TYPE     121       11        31        9
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 1               121
  STAGE II                0                11
  STAGE III              11                31
  STAGE IV                3                 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                 T1  T2 T3+T4
  1Q GAIN MUTATED     2   0    13
  1Q GAIN WILD-TYPE 128  18    37
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1                  2               128
  T2                  0                18
  T3+T4              13                37
[1] 3 2
[1] 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    4  6  1
  1Q GAIN WILD-TYPE 29 14  3
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0               4                29
  N1               6                14
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  1Q GAIN MUTATED    5  2  8
  1Q GAIN WILD-TYPE 76  6 88
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0               5                76
  M1               2                 6
  MX               8                88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     8   7
  1Q GAIN WILD-TYPE  50 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      8    7
  1Q GAIN WILD-TYPE   50  133
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               8                50
  MALE                 7               133
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
[1] "Remove cluster labels:" "1Q GAIN MUTATED"       
clus
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                2                22 
       TCGA-A4-A48D        TCGA-B1-A654        TCGA-B9-A44B        TCGA-B9-A69E 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GL-7773        TCGA-GL-A59T        TCGA-HE-A5NI        TCGA-HE-A5NJ 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E7 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-P4-A5EB        TCGA-PJ-A5Z9        TCGA-SX-A71S        TCGA-SX-A71U 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SS        TCGA-Y8-A894 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A8RZ 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  0     0
  1Q GAIN WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                           1    13
  1Q GAIN WILD-TYPE                        48   116
D2V10, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      1                48
  WHITE                                         13               116
[1] 4 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, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     0  13
  1Q GAIN WILD-TYPE   9 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      0   13
  1Q GAIN WILD-TYPE    9  140
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              13               140
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    30   1
  2P GAIN WILD-TYPE 136   6
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               31               142 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                1                 6 
$`2P GAIN MUTATED`
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B3-A6W5 
         516            2          412           67          223           85 
TCGA-B9-4117 TCGA-B9-A44B TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7046 TCGA-DW-5561 
          14           64          364           84         2948          414 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-GL-7966 TCGA-GL-A59T 
          36          208         1575         1194          112           91 
TCGA-HE-A5NF TCGA-HE-A5NI TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE 
        2072          360          511           62          160          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5EB TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71V 
         161         1043         2584          174           57          508 
TCGA-SX-A7SQ 
         494 

$`2P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 
         118           87            4         1778         1636          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
         763         1357           26          595          659          747 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         108          510           14         1029          307          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
        1049          379         1536          857          803          627 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 
          35          460         1338          671          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
           5          102          167           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 
         792          771          403          233           29         3760 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 
         232          214          218          116          353         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        1093         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
          92         1240         2429         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
        1040          578          757           97           10            7 
TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
        1479         1059          765          446          786          279 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        1967         5925          393          841           32          178 
TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 
         408         1726          167          608          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         146            2            4          391          543          438 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         292           11          541          148         3035         2653 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL 
        2816          391         1079         1199          994          423 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 
        1973          102          925         1247          847          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
           2          186          181          205 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                 2 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             2948              5925 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            223.0             583.5 
[1] "2.0 - 2948.0 (223.0)" "2.0 - 5925.0 (583.5)"
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P GAIN MUTATED        22        2         6        6
  2P GAIN WILD-TYPE     100        9        36        6
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                22               100
  STAGE II                2                 9
  STAGE III               6                36
  STAGE IV                6                 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                 T1  T2 T3+T4
  2P GAIN MUTATED    22   5    10
  2P GAIN WILD-TYPE 108  13    40
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1                 22               108
  T2                  5                13
  T3+T4              10                40
[1] 3 2
[1] 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    5  7  1
  2P GAIN WILD-TYPE 28 13  3
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0               5                28
  N1               7                13
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  2P GAIN MUTATED   10  5 19
  2P GAIN WILD-TYPE 71  3 77
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              10                71
  M1               5                 3
  MX              19                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"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    12  25
  2P GAIN WILD-TYPE  46 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     12   25
  2P GAIN WILD-TYPE   46  115
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              12                46
  MALE                25               115
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  0     1
  2P GAIN WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                           7    26
  2P GAIN WILD-TYPE                        42   103
D3V10, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                      7                42
  WHITE                                         26               103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     2  31
  2P GAIN WILD-TYPE   7 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2   31
  2P GAIN WILD-TYPE    7  122
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              31               122
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    32   1
  2Q GAIN WILD-TYPE 134   6
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               33               140 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                1                 6 
$`2Q GAIN MUTATED`
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-AL-3471 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-7332 
         516            2          412         1357           67          223 
TCGA-B3-A6W5 TCGA-B9-4117 TCGA-B9-A44B TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7046 
          85           14           64          364           84         2948 
TCGA-DW-5561 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 
         414           36          208         1575         1194          786 
TCGA-GL-7966 TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-IA-A40U TCGA-IA-A40Y 
         112           91         2072          360          511           62 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5EB TCGA-PJ-A5Z9 
         160          885          161         1043         2584          174 
TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SQ 
          57          508          494 

$`2Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 
         118           87            4         1778         1636          923 
TCGA-AL-3473 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
         763           26          595          659          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
         510           14         1029          307          930         1049 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
         379         1536          857          803          627           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
         460         1338          671          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         102          167           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7048 
         771          403          233           29         3760         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 
         214          218          116          353         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6792 
         578          757           97           10            7         1479 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 
        1059          765          446          279         1967         5925 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-HE-A5NH TCGA-HE-A5NJ 
         393          841           32          178          408         1726 
TCGA-HE-A5NL TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         167          608          677          649          146            2 
TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
           4          391          543          438          292           11 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 
         541          148         3035         2653         2816          391 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1079         1199          994          423         1973          102 
TCGA-SX-A7SO TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
         925         1247          847          224            2          186 
TCGA-Y8-A898 TCGA-Y8-A8RZ 
         181          205 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                2                 2 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             2948              5925 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              360               580 
[1] "2.0 - 2948.0 (360.0)" "2.0 - 5925.0 (580.0)"
[1] "hr=" "1.3"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED        23        2         6        7
  2Q GAIN WILD-TYPE      99        9        36        5
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                23                99
  STAGE II                2                 9
  STAGE III               6                36
  STAGE IV                7                 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                 T1  T2 T3+T4
  2Q GAIN MUTATED    23   5    11
  2Q GAIN WILD-TYPE 107  13    39
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1                 23               107
  T2                  5                13
  T3+T4              11                39
[1] 3 2
[1] 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    5  7  2
  2Q GAIN WILD-TYPE 28 13  2
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0               5                28
  N1               7                13
  N2               2                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  2Q GAIN MUTATED   11  5 20
  2Q GAIN WILD-TYPE 70  3 76
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0              11                70
  M1               5                 3
  MX              20                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"
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    13  26
  2Q GAIN WILD-TYPE  45 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     13   26
  2Q GAIN WILD-TYPE   45  114
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              13                45
  MALE                26               114
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     1
  2Q GAIN WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                           7    28
  2Q GAIN WILD-TYPE                        42   101
D4V10, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                      7                42
  WHITE                                         28               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     2  33
  2Q GAIN WILD-TYPE   7 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   33
  2Q GAIN WILD-TYPE    7  120
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              33               120
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    49   0
  3P GAIN WILD-TYPE 117   7
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               49               124 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                0                 7 
$`3P GAIN MUTATED`
TCGA-A4-7287 TCGA-A4-8311 TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
          21          729           23          600          436          379 
TCGA-A4-A4ZT TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M 
         516         1636          412           67          223          659 
TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
         930           85          857           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-7046 
        1338          671          167         1454          792         2948 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         214          116          353         1093         1142          744 
TCGA-DW-7963 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6790 TCGA-GL-6846 TCGA-GL-A59T 
        1240           10            7         1575         5925           91 
TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NL TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
        2072          360          167          160          885          161 
TCGA-P4-A5E7 TCGA-PJ-A5Z9 TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SS 
        2653          174          508          102          494         1247 
TCGA-Y8-A895 
           2 

$`3P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8515 TCGA-A4-8517 
          49            2          140          780          709          597 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 
           2          118           87            4         1778          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 
         763         1357           26          595          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 
         510           14         1029          307         1049          379 
TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
        1536          803          627           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
           5          102           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 
        1938         1242          792          921          771          403 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 
         233           29          364           84         3760         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          232 
TCGA-BQ-7061 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
         218          414         3950          419          114          445 
TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
          92         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6792 
         578          757           97           36          208         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
        1194         1059          765          446          786          279 
TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        1967          393          112          841           32          178 
TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
         408         1726          511          608           62          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55W TCGA-MH-A55Z 
         649          146            2            4         1043          391 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
         543          438          292           11          541          148 
TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71R 
        3035         2584         2816          391           57         1079 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SU 
        1199          994          423         1973          925          847 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         224          186          181          205 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                 2 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             5925              3950 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              460               526 
[1] "2.0 - 5925.0 (460.0)" "2.0 - 3950.0 (526.0)"
[1] "hr="   "3e+08"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED        44        3         6        1
  3P GAIN WILD-TYPE      78        8        36       11
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                44                78
  STAGE II                3                 8
  STAGE III               6                36
  STAGE IV                1                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                T1 T2 T3+T4
  3P GAIN MUTATED   45  6     7
  3P GAIN WILD-TYPE 85 12    43
D5V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1                 45                85
  T2                  6                12
  T3+T4               7                43
[1] 3 2
[1] 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    6  2  0
  3P GAIN WILD-TYPE 27 18  4
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0               6                27
  N1               2                18
  N2               0                 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 MX
  3P GAIN MUTATED   24  0 29
  3P GAIN WILD-TYPE 57  8 67
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0              24                57
  M1               0                 8
  MX              29                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"
D5V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   15 43
  3P GAIN WILD-TYPE 43 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     15   43
  3P GAIN WILD-TYPE   43   97
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              15                43
  MALE                43                97
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  1     1
  3P GAIN WILD-TYPE                                1     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                          12    38
  3P GAIN WILD-TYPE                        37    91
D5V10, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                     12                37
  WHITE                                         38                91
[1] 4 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, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     2  46
  3P GAIN WILD-TYPE   7 107
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   46
  3P GAIN WILD-TYPE    7  107
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              46               107
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    58   1
  3Q GAIN WILD-TYPE 108   6
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               59               114 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                 6 
$`3Q GAIN MUTATED`
TCGA-A4-7287 TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8518 
          21            2          729          709           23          600 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-AL-3468 TCGA-AL-3471 
         436          379          516            2         1636          412 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4114 
          67          223          659          930           85          857 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
          14           35          460         1338          671           64 
TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-7046 TCGA-BQ-7060 
         167         1454          792          233         2948          214 
TCGA-BQ-7062 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6132 
         116         1093         1142          744         1240         2460 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-A8LD 
        1670         1040           10            7         1575         1967 
TCGA-GL-6846 TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NL TCGA-KV-A6GD 
        5925           91         2072          360          167          160 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         885          161         3035         2653          174           57 
TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-Y8-A895 
         508          102          494         1247            2 

$`3Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8517 TCGA-A4-A5Y0 TCGA-A4-A5Y1 
          49          140          780          597          118           87 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
           4         1778          923          763         1357           26 
TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         595          747          108          510           14         1029 
TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 
         307         1049          379         1536          803          627 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 
         585          207            5          102           52         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         586          270         1938         1242          792          921 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         771          403           29          364           84         3760 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 
         232          218          353          414         3950          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6134 TCGA-EV-5902 
         114          445           92         2429         1856          578 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6795 
         757           97           36          208         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-7773 
        1059          765          446          786          279          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-HE-A5NH TCGA-HE-A5NJ 
         112          841           32          178          408         1726 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         511          608           62          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
           2            4         1043          391          543          438 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5EB TCGA-P4-A5ED 
         292           11          541          148         2584         2816 
TCGA-PJ-A5Z8 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM 
         391         1079         1199          994          423         1973 
TCGA-SX-A7SO TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         925          847          224          186          181          205 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                 2 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             5925              3950 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            494.0             510.5 
[1] "2.0 - 5925.0 (494.0)" "2.0 - 3950.0 (510.5)"
[1] "hr=" "3.6"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED        48        4        11        1
  3Q GAIN WILD-TYPE      74        7        31       11
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                48                74
  STAGE II                4                 7
  STAGE III              11                31
  STAGE IV                1                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                T1 T2 T3+T4
  3Q GAIN MUTATED   50  7    11
  3Q GAIN WILD-TYPE 80 11    39
D6V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1                 50                80
  T2                  7                11
  T3+T4              11                39
[1] 3 2
[1] 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    7  4  0
  3Q GAIN WILD-TYPE 26 16  4
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0               7                26
  N1               4                16
  N2               0                 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 MX
  3Q GAIN MUTATED   26  0 36
  3Q GAIN WILD-TYPE 55  8 60
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              26                55
  M1               0                 8
  MX              36                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"
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   17 51
  3Q GAIN WILD-TYPE 41 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     17   51
  3Q GAIN WILD-TYPE   41   89
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              17                41
  MALE                51                89
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  2     1
  3Q GAIN WILD-TYPE                                0     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                          15    42
  3Q GAIN WILD-TYPE                        34    87
D6V10, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                     15                34
  WHITE                                         42                87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     2  53
  3Q GAIN WILD-TYPE   7 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2   53
  3Q GAIN WILD-TYPE    7  100
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              53               100
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     4   1
  4P GAIN WILD-TYPE 162   6
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5               168 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                 6 
$`4P GAIN MUTATED`
TCGA-B9-4114 TCGA-B9-A5W9 TCGA-BQ-5892 TCGA-G7-6789 TCGA-G7-6795 
         857            5          364          208         1194 

$`4P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
         516            2          118           87            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
        1636          412          923          763         1357           26 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
          67          595          223          659          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
         510           14         1029          307          930         1049 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
         379           85         1536          803          627           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
          35          460         1338          671           64          585 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
         207          102          167           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 
         792          771          403          233           29           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         419          114          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        2460         1856         1670         1040          578          757 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 
          97           10            7           36         1575         1479 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD 
        1059          765          446          786          279         1967 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         511          608           62          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
           2            4          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         174           57         1079         1199          994          508 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS 
         423         1973          102          925          494         1247 
TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         847          224            2          186          181          205 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5                 2 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             1194              5925 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
              364               509 
[1] "5.0 - 1194.0 (364.0)" "2.0 - 5925.0 (509.0)"
[1] "hr=" "11" 
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED         3        0         0        2
  4P GAIN WILD-TYPE     119       11        42       10
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 3               119
  STAGE II                0                11
  STAGE III               0                42
  STAGE IV                2                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                 T1  T2 T3+T4
  4P GAIN MUTATED     3   1     2
  4P GAIN WILD-TYPE 127  17    48
D7V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1                  3               127
  T2                  1                17
  T3+T4               2                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"
                   vv
clus                N0 N1 N2
  4P GAIN MUTATED    2  1  1
  4P GAIN WILD-TYPE 31 19  3
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               2                31
  N1               1                19
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  4P GAIN MUTATED    1  1  3
  4P GAIN WILD-TYPE 80  7 93
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               1                80
  M1               1                 7
  MX               3                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1   5
  4P GAIN WILD-TYPE  57 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    5
  4P GAIN WILD-TYPE   57  135
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               1                57
  MALE                 5               135
[1] 2 2
[1] FALSE
D7V8, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                51 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8310        TCGA-A4-8311 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-8312        TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A4ZT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963        TCGA-EV-5901 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-A4TM        TCGA-G7-A8LD        TCGA-IA-A40U        TCGA-IA-A40X 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IA-A40Y        TCGA-J7-8537        TCGA-Q2-A5QZ        TCGA-SX-A71R 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SN        TCGA-SX-A7SO        TCGA-SX-A7SP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-SX-A7SQ        TCGA-SX-A7SS        TCGA-SX-A7SU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     0
  4P GAIN WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           1     5
  4P GAIN WILD-TYPE                        48   124
D7V10, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      1                48
  WHITE                                          5               124
[1] 4 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, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0   6
  4P GAIN WILD-TYPE   9 147
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    6
  4P GAIN WILD-TYPE    9  147
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               6               147
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     4   1
  4Q GAIN WILD-TYPE 162   6
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               168 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                 6 
$`4Q GAIN MUTATED`
TCGA-B9-4114 TCGA-B9-A5W9 TCGA-BQ-5892 TCGA-G7-6789 TCGA-G7-6795 
         857            5          364          208         1194 

$`4Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
         516            2          118           87            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
        1636          412          923          763         1357           26 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
          67          595          223          659          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
         510           14         1029          307          930         1049 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
         379           85         1536          803          627           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
          35          460         1338          671           64          585 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
         207          102          167           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 
         792          771          403          233           29           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         419          114          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        2460         1856         1670         1040          578          757 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 
          97           10            7           36         1575         1479 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD 
        1059          765          446          786          279         1967 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         511          608           62          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
           2            4          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         174           57         1079         1199          994          508 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS 
         423         1973          102          925          494         1247 
TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         847          224            2          186          181          205 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5                 2 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             1194              5925 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
              364               509 
[1] "5.0 - 1194.0 (364.0)" "2.0 - 5925.0 (509.0)"
[1] "hr=" "11" 
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED         3        0         0        1
  4Q GAIN WILD-TYPE     119       11        42       11
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 3               119
  STAGE II                0                11
  STAGE III               0                42
  STAGE IV                1                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                 T1  T2 T3+T4
  4Q GAIN MUTATED     3   1     1
  4Q GAIN WILD-TYPE 127  17    49
D8V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1                  3               127
  T2                  1                17
  T3+T4               1                49
[1] 3 2
[1] 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    2  0  1
  4Q GAIN WILD-TYPE 31 20  3
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               2                31
  N1               0                20
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  4Q GAIN MUTATED    1  0  3
  4Q GAIN WILD-TYPE 80  8 93
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               1                80
  M1               0                 8
  MX               3                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1   4
  4Q GAIN WILD-TYPE  57 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    4
  4Q GAIN WILD-TYPE   57  136
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               1                57
  MALE                 4               136
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     0
  4Q GAIN WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           1     4
  4Q GAIN WILD-TYPE                        48   125
D8V10, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      1                48
  WHITE                                          4               125
[1] 4 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, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   5
  4Q GAIN WILD-TYPE   9 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    5
  4Q GAIN WILD-TYPE    9  148
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               5               148
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    22   1
  5P GAIN WILD-TYPE 144   6
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               23               150 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                1                 6 
$`5P GAIN MUTATED`
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8516 TCGA-A4-A48D TCGA-AL-3473 TCGA-B1-5398 
           2          140           23          379          763          595 
TCGA-B1-A656 TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 
          14           14            5          771           29          364 
TCGA-DW-7838 TCGA-DZ-6131 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-GL-A4EM 
         744         2429          578           10          208           32 
TCGA-IA-A40Y TCGA-KV-A6GD TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SQ 
          62          160         2584           57          494 

$`5P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8517 
           7           49          780          729          709          597 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         600          436          516            2          118           87 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 
           4         1778         1636          412          923         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
          26           67          223          659          747          108 
TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
         510         1029          307          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
          85         1536          857          803          627           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         102          167           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 
         403          233           84         3760         2948         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1093         1142          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
        1240         2460         1856         1670         1040          757 
TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
          97            7           36         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD 
        1059          765          446          786          279         1967 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T 
        5925          393          112          841          178           91 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         1726          167          511 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
         608          677          649          146            2            4 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          391          543          438 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         292           11          541          148         3035         2653 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          391          174         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SS 
         508          423         1973          102          925         1247 
TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         847          224            2          186          181          205 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                 2 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             2584              5925 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              160               542 
[1] "2.0 - 2584.0 (160.0)" "2.0 - 5925.0 (542.0)"
[1] "hr=" "1.4"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED        14        1         8        3
  5P GAIN WILD-TYPE     108       10        34        9
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                14               108
  STAGE II                1                10
  STAGE III               8                34
  STAGE IV                3                 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                 T1  T2 T3+T4
  5P GAIN MUTATED    14   3    10
  5P GAIN WILD-TYPE 116  15    40
D9V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1                 14               116
  T2                  3                15
  T3+T4              10                40
[1] 3 2
[1] 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    8  2  1
  5P GAIN WILD-TYPE 25 18  3
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0               8                25
  N1               2                18
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  5P GAIN MUTATED   12  2 12
  5P GAIN WILD-TYPE 69  6 84
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              12                69
  M1               2                 6
  MX              12                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     7  20
  5P GAIN WILD-TYPE  51 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7   20
  5P GAIN WILD-TYPE   51  120
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               7                51
  MALE                20               120
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  0     1
  5P GAIN WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                           4    20
  5P GAIN WILD-TYPE                        45   109
D9V10, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                      4                45
  WHITE                                         20               109
[1] 4 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, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     0  22
  5P GAIN WILD-TYPE   9 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      0   22
  5P GAIN WILD-TYPE    9  131
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              22               131
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    22   1
  5Q GAIN WILD-TYPE 144   6
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               23               150 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1                 6 
$`5Q GAIN MUTATED`
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8516 TCGA-A4-A48D TCGA-AL-3473 TCGA-B1-5398 
           2          140           23          379          763          595 
TCGA-B1-A656 TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 
          14           14            5          771           29          364 
TCGA-DW-7838 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-GL-A4EM TCGA-IA-A40Y 
         744          578           10          208           32           62 
TCGA-KV-A6GD TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SQ 
         160         3035         2584           57          494 

$`5Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8517 
           7           49          780          729          709          597 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         600          436          516            2          118           87 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 
           4         1778         1636          412          923         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
          26           67          223          659          747          108 
TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
         510         1029          307          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
          85         1536          857          803          627           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         102          167           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 
         403          233           84         3760         2948         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1093         1142          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 
         757           97            7           36         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
        1194         1059          765          446          786          279 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R 
        1967         5925          393          112          841          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         511          608          677          649          146            2 
TCGA-J7-8537 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
           4          885          161         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E7 
         438          292           11          541          148         2653 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          391          174         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SS 
         508          423         1973          102          925         1247 
TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         847          224            2          186          181          205 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                 2 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             3035              5925 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              160               542 
[1] "2.0 - 3035.0 (160.0)" "2.0 - 5925.0 (542.0)"
[1] "hr=" "1.4"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED        14        1         8        3
  5Q GAIN WILD-TYPE     108       10        34        9
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                14               108
  STAGE II                1                10
  STAGE III               8                34
  STAGE IV                3                 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                 T1  T2 T3+T4
  5Q GAIN MUTATED    15   3     9
  5Q GAIN WILD-TYPE 115  15    41
D10V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1                 15               115
  T2                  3                15
  T3+T4               9                41
[1] 3 2
[1] 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    7  3  1
  5Q GAIN WILD-TYPE 26 17  3
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0               7                26
  N1               3                17
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  5Q GAIN MUTATED   12  2 12
  5Q GAIN WILD-TYPE 69  6 84
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0              12                69
  M1               2                 6
  MX              12                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     7  20
  5Q GAIN WILD-TYPE  51 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7   20
  5Q GAIN WILD-TYPE   51  120
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               7                51
  MALE                20               120
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     1
  5Q GAIN WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           5    19
  5Q GAIN WILD-TYPE                        44   110
D10V10, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                      5                44
  WHITE                                         19               110
[1] 4 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, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  23
  5Q GAIN WILD-TYPE   9 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   23
  5Q GAIN WILD-TYPE    9  130
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              23               130
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED     5   0
  6P GAIN WILD-TYPE 161   7
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                5               168 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                0                 7 
$`6P GAIN MUTATED`
TCGA-AL-A5DJ TCGA-B9-A69E TCGA-BQ-7048 TCGA-DW-5561 TCGA-Q2-A5QZ 
          26          102         2839          414           57 

$`6P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
         516            2          118           87            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        1636          412          923          763         1357           67 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
         595          223          659          747          108          510 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
          14         1029          307          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
          85         1536          857          803          627           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
          35          460         1338          671           64          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
         207            5          167           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         792          771          403          233           29          364 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
          84         3760         2948         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          232          214          218          116 
TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         353         3950         1093         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92         1240         2429         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
        1856         1670         1040          578          757           97 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
          10            7           36          208         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
        1194         1059          765          446          786          279 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        1967         5925          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
         167          511          608           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         146            2            4          160          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          391          543          438          292           11 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         541          148         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         391          174         1079         1199          994          508 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS 
         423         1973          102          925          494         1247 
TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         847          224            2          186          181          205 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               26                 2 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             2839              5925 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            102.0             510.5 
[1] "26.0 - 2839.0 (102.0)" "2.0 - 5925.0 (510.5)" 
[1] "hr="     "2.6e+07"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P GAIN MUTATED         1        0         5        2
  6P GAIN WILD-TYPE     121       11        37       10
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 1               121
  STAGE II                0                11
  STAGE III               5                37
  STAGE IV                2                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                 T1  T2 T3+T4
  6P GAIN MUTATED     1   0     7
  6P GAIN WILD-TYPE 129  18    43
D11V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1                  1               129
  T2                  0                18
  T3+T4               7                43
[1] 3 2
[1] 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    1  3  0
  6P GAIN WILD-TYPE 32 17  4
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0               1                32
  N1               3                17
  N2               0                 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 MX
  6P GAIN MUTATED    2  2  3
  6P GAIN WILD-TYPE 79  6 93
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0               2                79
  M1               2                 6
  MX               3                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     3   5
  6P GAIN WILD-TYPE  55 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3    5
  6P GAIN WILD-TYPE   55  135
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               3                55
  MALE                 5               135
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, continuous
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                2                22 
       TCGA-A4-A48D        TCGA-B1-A654        TCGA-B9-A44B        TCGA-G7-A8LD 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GL-7773        TCGA-GL-A59T        TCGA-HE-A5NI        TCGA-HE-A5NJ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E7 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-P4-A5EB        TCGA-PJ-A5Z9        TCGA-SX-A71S        TCGA-SX-A71U 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SS        TCGA-Y8-A894 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A8RZ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0     0
  6P GAIN WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           2     6
  6P GAIN WILD-TYPE                        47   123
D11V10, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      2                47
  WHITE                                          6               123
[1] 4 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, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     0   8
  6P GAIN WILD-TYPE   9 145
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0    8
  6P GAIN WILD-TYPE    9  145
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               8               145
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED     3   0
  6Q GAIN WILD-TYPE 163   7
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3               170 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                0                 7 
$`6Q GAIN MUTATED`
TCGA-AL-A5DJ TCGA-DW-5561 TCGA-Q2-A5QZ 
          26          414           57 

$`6Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
         516            2          118           87            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        1636          412          923          763         1357           67 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
         595          223          659          747          108          510 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
          14         1029          307          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
          85         1536          857          803          627           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
          35          460         1338          671           64          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
         207            5          102          167           52         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
         586          270         1938         1454         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
         921          792          771          403          233           29 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
         364           84         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1533         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         218          116          353         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        2429         2460         1856         1670         1040          578 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 
         757           97           10            7           36          208 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
        1575         1479         1194         1059          765          446 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         786          279         1967         5925          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
         841           32          178           91         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
         360         1726          167          511          608           62 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
         677          649          146            2            4          160 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          391          543          438 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         292           11          541          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
        2584         2816          391          174         1079         1199 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
         994          508          423         1973          102          925 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
         494         1247          847          224            2          186 
TCGA-Y8-A898 TCGA-Y8-A8RZ 
         181          205 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               26                 2 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              414              5925 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             57.0             510.5 
[1] "26.0 - 414.0 (57.0)"  "2.0 - 5925.0 (510.5)"
[1] "hr="     "3300000"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED         1        0         3        2
  6Q GAIN WILD-TYPE     121       11        39       10
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 1               121
  STAGE II                0                11
  STAGE III               3                39
  STAGE IV                2                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                 T1  T2 T3+T4
  6Q GAIN MUTATED     1   0     5
  6Q GAIN WILD-TYPE 129  18    45
D12V4, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1                  1               129
  T2                  0                18
  T3+T4               5                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"
                   vv
clus                N0 N1 N2
  6Q GAIN MUTATED    0  3  0
  6Q GAIN WILD-TYPE 33 17  4
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0               0                33
  N1               3                17
  N2               0                 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 MX
  6Q GAIN MUTATED    1  2  3
  6Q GAIN WILD-TYPE 80  6 93
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0               1                80
  M1               2                 6
  MX               3                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     3   3
  6Q GAIN WILD-TYPE  55 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3    3
  6Q GAIN WILD-TYPE   55  137
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               3                55
  MALE                 3               137
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                23 
       TCGA-A4-A48D        TCGA-B1-A654        TCGA-B9-A44B        TCGA-B9-A69E 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-GL-7773        TCGA-GL-A59T        TCGA-HE-A5NI 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HE-A5NJ        TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9        TCGA-SX-A71S 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SS 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RZ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     0
  6Q GAIN WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           2     4
  6Q GAIN WILD-TYPE                        47   125
D12V10, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      2                47
  WHITE                                          4               125
[1] 4 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, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     0   6
  6Q GAIN WILD-TYPE   9 147
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0    6
  6Q GAIN WILD-TYPE    9  147
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               6               147
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   105   3
  7P GAIN WILD-TYPE  61   4
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              108                65 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                3                 4 
$`7P GAIN MUTATED`
TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 
         493          582           27           49            2          780 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT 
         729          709           23          597          436          516 
TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 
           2            4         1636          412          923         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 
          26           67          659          747          108           14 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
        1029          930          379           85         1536          857 
TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         803           14           35          460         1338          671 
TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5891 
         585          167         1454          792          771           29 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 
          84         3760         2948         1533          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         218          116          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
        1142          744          114          445           92         1240 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF 
        2460         1856         1040          757           10            7 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 TCGA-G7-A4TM 
          36          208         1575         1194          786          279 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        5925          112          841          178           91         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40Y TCGA-IZ-8196 
         408          360         1726          167           62          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         146            2          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         391          292          148         2653          174           57 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN 
        1079         1199          994          508         1973          102 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
         494         1247          847            2          186          181 

$`7P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8518 
         554           21            3            7          140          600 
TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 
         379          118           87         1778          763          595 
TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A44B 
         223          510          307         1049          627           64 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
         207            5          102           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 
         270         1938         1242          921          792          403 
TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 
         233          364         2839         1864         1516          799 
TCGA-BQ-7056 TCGA-DW-7839 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ 
         612          419         2429         1670          578           97 
TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7773 
        1479         1059          765          446         1967          393 
TCGA-GL-A4EM TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-J7-8537 TCGA-MH-A560 
          32          511          608          677            4          543 
TCGA-MH-A561 TCGA-MH-A854 TCGA-MH-A856 TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-P4-A5ED 
         438           11          541         3035         2584         2816 
TCGA-PJ-A5Z8 TCGA-SX-A7SL TCGA-SX-A7SO TCGA-Y8-A894 TCGA-Y8-A8RZ 
         391          423          925          224          205 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                2                 3 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             5925              3035 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            476.5             541.0 
[1] "2.0 - 5925.0 (476.5)" "3.0 - 3035.0 (541.0)"
[1] "hr=" "1.8"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED        85        4        15        8
  7P GAIN WILD-TYPE      37        7        27        4
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                85                37
  STAGE II                4                 7
  STAGE III              15                27
  STAGE IV                8                 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"
                   vv
clus                T1 T2 T3+T4
  7P GAIN MUTATED   88 10    22
  7P GAIN WILD-TYPE 42  8    28
D13V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1                 88                42
  T2                 10                 8
  T3+T4              22                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                N0 N1 N2
  7P GAIN MUTATED   16  7  2
  7P GAIN WILD-TYPE 17 13  2
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              16                17
  N1               7                13
  N2               2                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  7P GAIN MUTATED   45  5 61
  7P GAIN WILD-TYPE 36  3 35
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              45                36
  M1               5                 3
  MX              61                35
[1] 3 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   30 90
  7P GAIN WILD-TYPE 28 50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     30   90
  7P GAIN WILD-TYPE   28   50
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              30                28
  MALE                90                50
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  2     3
  7P GAIN WILD-TYPE                                0     1
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                          29    75
  7P GAIN WILD-TYPE                        20    54
D13V10, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          3                 1
  BLACK OR AFRICAN AMERICAN                     29                20
  WHITE                                         75                54
[1] 4 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, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    4 97
  7P GAIN WILD-TYPE  5 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4   97
  7P GAIN WILD-TYPE    5   56
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO              97                56
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   106   3
  7Q GAIN WILD-TYPE  60   4
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              109                64 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                3                 4 
$`7Q GAIN MUTATED`
TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 
         493          582           27           49            2          780 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT 
         729          709           23          597          436          516 
TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 
           2            4         1636          412          923         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 
          26           67          659          747          108           14 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
        1029          930          379           85         1536          857 
TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         803           14           35          460         1338          671 
TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5891 
         585          167         1454          792          771           29 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7059 
         364           84         3760         2948         1533          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1093         1142          744          114          445           92 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 
        1240         2460         1856         1040          757           10 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 
           7           36          208         1575         1194          786 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T 
         279         5925          112          841          178           91 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40Y 
        2072          408          360         1726          167           62 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         649          146            2          160          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-PJ-A5Z9 
        1043          391          292          148         2653          174 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM 
          57         1079         1199          994          508         1973 
TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A895 TCGA-Y8-A896 
         102          494         1247          847            2          186 
TCGA-Y8-A898 
         181 

$`7Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8518 
         554           21            3            7          140          600 
TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 
         379          118           87         1778          763          595 
TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A44B 
         223          510          307         1049          627           64 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
         207            5          102           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 
         270         1938         1242          921          792          403 
TCGA-BQ-5890 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
         233         2839         1864         1516          799          612 
TCGA-DW-7839 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-G7-6792 
         419         2429         1670          578           97         1479 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-A4EM 
        1059          765          446         1967          393           32 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-J7-8537 TCGA-MH-A560 TCGA-MH-A561 
         511          608          677            4          543          438 
TCGA-MH-A854 TCGA-MH-A856 TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
          11          541         3035         2584         2816          391 
TCGA-SX-A7SL TCGA-SX-A7SO TCGA-Y8-A894 TCGA-Y8-A8RZ 
         423          925          224          205 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                2                 3 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             5925              3035 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              460               542 
[1] "2.0 - 5925.0 (460.0)" "3.0 - 3035.0 (542.0)"
[1] "hr=" "1.9"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED        86        4        15        8
  7Q GAIN WILD-TYPE      36        7        27        4
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                86                36
  STAGE II                4                 7
  STAGE III              15                27
  STAGE IV                8                 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"
                   vv
clus                T1 T2 T3+T4
  7Q GAIN MUTATED   89 10    22
  7Q GAIN WILD-TYPE 41  8    28
D14V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1                 89                41
  T2                 10                 8
  T3+T4              22                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                N0 N1 N2
  7Q GAIN MUTATED   17  7  2
  7Q GAIN WILD-TYPE 16 13  2
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              17                16
  N1               7                13
  N2               2                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  7Q GAIN MUTATED   46  5 61
  7Q GAIN WILD-TYPE 35  3 35
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              46                35
  M1               5                 3
  MX              61                35
[1] 3 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   30 91
  7Q GAIN WILD-TYPE 28 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     30   91
  7Q GAIN WILD-TYPE   28   49
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              30                28
  MALE                91                49
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  2     3
  7Q GAIN WILD-TYPE                                0     1
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                          29    76
  7Q GAIN WILD-TYPE                        20    53
D14V10, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          3                 1
  BLACK OR AFRICAN AMERICAN                     29                20
  WHITE                                         76                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    4 98
  7Q GAIN WILD-TYPE  5 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4   98
  7Q GAIN WILD-TYPE    5   55
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO              98                55
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED     9   1
  8P GAIN WILD-TYPE 157   6
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               10               163 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                1                 6 
$`8P GAIN MUTATED`
TCGA-A4-8630 TCGA-AL-3471 TCGA-B9-A5W9 TCGA-BQ-5887 TCGA-BQ-7056 TCGA-G7-6789 
         436          412            5          771          612          208 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-IZ-8195 TCGA-SX-A71U 
         112           32          677          994 

$`8P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A4ZT 
         709           23          597          600          379          516 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         102          167           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         403          233           29          364           84         3760 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2948         2839         1864         1533         1516          799 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
         445           92         1240         2429         2460         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
        1670         1040          578          757           97           10 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
           7           36         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 
         765          446          786          279         1967         5925 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
         393          841          178           91         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
         360         1726          167          511          608           62 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
         649          146            2            4          160          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          391          543          438          292 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
          11          541          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
        2816          391          174           57         1079         1199 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         508          423         1973          102          925          494 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
        1247          847          224            2          186          181 
TCGA-Y8-A8RZ 
         205 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                5                 2 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              994              5925 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              424               510 
[1] "5.0 - 994.0 (424.0)"  "2.0 - 5925.0 (510.0)"
[1] "hr=" "5.6"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         5        1         5        1
  8P GAIN WILD-TYPE     117       10        37       11
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 5               117
  STAGE II                1                10
  STAGE III               5                37
  STAGE IV                1                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                 T1  T2 T3+T4
  8P GAIN MUTATED     5   1     6
  8P GAIN WILD-TYPE 125  17    44
D15V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1                  5               125
  T2                  1                17
  T3+T4               6                44
[1] 3 2
[1] 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    2  3  1
  8P GAIN WILD-TYPE 31 17  3
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0               2                31
  N1               3                17
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  8P GAIN MUTATED    5  0  7
  8P GAIN WILD-TYPE 76  8 89
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               5                76
  M1               0                 8
  MX               7                89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     5   7
  8P GAIN WILD-TYPE  53 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    7
  8P GAIN WILD-TYPE   53  133
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               5                53
  MALE                 7               133
[1] 2 2
[1] FALSE
D15V8, continuous
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                50 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8310        TCGA-A4-8311 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-8312        TCGA-A4-8518        TCGA-A4-A4ZT        TCGA-A4-A57E 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963        TCGA-EV-5901 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-A4TM        TCGA-G7-A8LD        TCGA-IA-A40U        TCGA-IA-A40X 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-IA-A40Y        TCGA-J7-8537        TCGA-Q2-A5QZ        TCGA-SX-A71R 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-SX-A7SN        TCGA-SX-A7SO        TCGA-SX-A7SP        TCGA-SX-A7SQ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-SX-A7SU 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
D15V9, continuous
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                1                23 
       TCGA-A4-A48D        TCGA-B1-A654        TCGA-B9-A44B        TCGA-B9-A69E 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-GL-7773        TCGA-GL-A59T        TCGA-HE-A5NI 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HE-A5NJ        TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9        TCGA-Q2-A5QZ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SS 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RZ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     0
  8P GAIN WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           0    12
  8P GAIN WILD-TYPE                        49   117
D15V10, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      0                49
  WHITE                                         12               117
[1] 4 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, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     0  10
  8P GAIN WILD-TYPE   9 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0   10
  8P GAIN WILD-TYPE    9  143
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              10               143
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    12   1
  8Q GAIN WILD-TYPE 154   6
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               13               160 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                1                 6 
$`8Q GAIN MUTATED`
TCGA-A4-8630 TCGA-AL-3471 TCGA-B9-A5W9 TCGA-BQ-5887 TCGA-BQ-7056 TCGA-F9-A8NY 
         436          412            5          771          612           36 
TCGA-G7-6789 TCGA-GL-7966 TCGA-GL-A4EM TCGA-IA-A40Y TCGA-IZ-8195 TCGA-Q2-A5QZ 
         208          112           32           62          677           57 
TCGA-SX-A71U 
         994 

$`8Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A4ZT 
         709           23          597          600          379          516 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         102          167           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         403          233           29          364           84         3760 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2948         2839         1864         1533         1516          799 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
         445           92         1240         2429         2460         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
        1670         1040          578          757           97           10 
TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
           7         1575         1479         1194         1059          765 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 
         446          786          279         1967         5925          393 
TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
         841          178           91         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8196 TCGA-IZ-A6M8 
        1726          167          511          608          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
           2            4          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
         174         1079         1199          508          423         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 
         102          925          494         1247          847          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
           2          186          181          205 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                5                 2 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              994              5925 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            208.0             513.5 
[1] "5.0 - 994.0 (208.0)"  "2.0 - 5925.0 (513.5)"
[1] "hr=" "5.6"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED         5        1         7        4
  8Q GAIN WILD-TYPE     117       10        35        8
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 5               117
  STAGE II                1                10
  STAGE III               7                35
  STAGE IV                4                 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                 T1  T2 T3+T4
  8Q GAIN MUTATED     5   1    11
  8Q GAIN WILD-TYPE 125  17    39
D16V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1                  5               125
  T2                  1                17
  T3+T4              11                39
[1] 3 2
[1] 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    2  6  2
  8Q GAIN WILD-TYPE 31 14  2
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0               2                31
  N1               6                14
  N2               2                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  8Q GAIN MUTATED    5  2 10
  8Q GAIN WILD-TYPE 76  6 86
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0               5                76
  M1               2                 6
  MX              10                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     9   8
  8Q GAIN WILD-TYPE  49 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      9    8
  8Q GAIN WILD-TYPE   49  132
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               9                49
  MALE                 8               132
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
[1] "Remove cluster labels:" "8Q GAIN MUTATED"       
clus
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                22 
       TCGA-A4-A48D        TCGA-B1-A654        TCGA-B9-A44B        TCGA-B9-A69E 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-GL-7773        TCGA-GL-A59T        TCGA-HE-A5NI 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-HE-A5NJ        TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9        TCGA-SX-A71S 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SS        TCGA-Y8-A894 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A8RZ 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     1
  8Q GAIN WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                           1    15
  8Q GAIN WILD-TYPE                        48   114
D16V10, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                      1                48
  WHITE                                         15               114
[1] 4 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, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     0  15
  8Q GAIN WILD-TYPE   9 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      0   15
  8Q GAIN WILD-TYPE    9  138
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              15               138
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     2   0
  9P GAIN WILD-TYPE 164   7
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2               171 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                 7 
$`9P GAIN MUTATED`
TCGA-B3-4104 TCGA-GL-7966 
        1049          112 

$`9P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
         516            2          118           87            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
        1636          412          923          763         1357           26 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
          67          595          223          659          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 
         510           14         1029          307          930          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
          85         1536          857          803          627           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
          35          460         1338          671           64          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
         207            5          102          167           52         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
         586          270         1938         1454         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
         921          792          771          403          233           29 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
         364           84         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1533         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         218          116          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
         578          757           97           10            7           36 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
         208         1575         1479         1194         1059          765 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 
         446          786          279         1967         5925          393 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
         841           32          178           91         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
         360         1726          167          511          608           62 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
         677          649          146            2            4          160 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          391          543          438 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         292           11          541          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        2584         2816          391          174           57         1079 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1199          994          508          423         1973          102 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 
         925          494         1247          847          224            2 
TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         186          181          205 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              112                 2 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1049              5925 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            580.5             508.0 
[1] "112.0 - 1049.0 (580.5)" "2.0 - 5925.0 (508.0)"  
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P GAIN MUTATED         0        1         2        0
  9P GAIN WILD-TYPE     122       10        40       12
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 0               122
  STAGE II                1                10
  STAGE III               2                40
  STAGE IV                0                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                 T1  T2 T3+T4
  9P GAIN MUTATED     0   1     2
  9P GAIN WILD-TYPE 130  17    48
D17V4, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1                  0               130
  T2                  1                17
  T3+T4               2                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"
                   vv
clus                N0 N1 N2
  9P GAIN MUTATED    0  1  1
  9P GAIN WILD-TYPE 33 19  3
D17V5, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                55 
       TCGA-A4-7583        TCGA-A4-7585        TCGA-A4-7915        TCGA-A4-A57E 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A4-A5Y1        TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-3473 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-A655        TCGA-B1-A656 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5882        TCGA-BQ-5885        TCGA-BQ-5887 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7045 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7056 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-F9-A8NY        TCGA-G7-6789 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501        TCGA-G7-A8LD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GL-6846        TCGA-GL-A59R        TCGA-IA-A40U        TCGA-IA-A40Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-J7-6720        TCGA-J7-8537        TCGA-KV-A74V        TCGA-P4-A5E6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-P4-A5E8        TCGA-P4-A5EA        TCGA-SX-A71R        TCGA-SX-A7SM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-SX-A7SP        TCGA-SX-A7SS        TCGA-Y8-A8RZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
                   vv
clus                M0 M1 MX
  9P GAIN MUTATED    2  0  1
  9P GAIN WILD-TYPE 79  8 95
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0               2                79
  M1               0                 8
  MX               1                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1   2
  9P GAIN WILD-TYPE  57 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1    2
  9P GAIN WILD-TYPE   57  138
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               1                57
  MALE                 2               138
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     0
  9P GAIN WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           0     3
  9P GAIN WILD-TYPE                        49   126
D17V10, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      0                49
  WHITE                                          3               126
[1] 4 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, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0   3
  9P GAIN WILD-TYPE   9 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0    3
  9P GAIN WILD-TYPE    9  150
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               3               150
[1] 2 2
[1] FALSE

Clustering(18) Variable = 10P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     6   0
  10P GAIN WILD-TYPE 160   7
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                167 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 0                  7 
$`10P GAIN MUTATED`
TCGA-A4-8098 TCGA-AL-3468 TCGA-B9-4617 TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-SX-A7SS 
         140         1636           35           10           36         1247 

$`10P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
           7           49            2          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 
           2          118           87            4         1778          412 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 
        1536          857          803          627           14          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1338          671           64          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         102          167           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
         771          403          233           29          364           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         419          114          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        2460         1856         1670         1040          578          757 
TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
          97            7          208         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD 
        1059          765          446          786          279         1967 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         511          608           62          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
           2            4          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         174           57         1079         1199          994          508 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SU 
         423         1973          102          925          494          847 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         224            2          186          181          205 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                10                  2 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1636               5925 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                88                510 
[1] "10.0 - 1636.0 (88.0)" "2.0 - 5925.0 (510.0)"
[1] "hr="     "9300000"
D18V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED         3        1         2        1
  10P GAIN WILD-TYPE     119       10        40       11
D18V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  3                119
  STAGE II                 1                 10
  STAGE III                2                 40
  STAGE IV                 1                 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                  T1  T2 T3+T4
  10P GAIN MUTATED     4   1     3
  10P GAIN WILD-TYPE 126  17    47
D18V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                   4                126
  T2                   1                 17
  T3+T4                3                 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"
                    vv
clus                 N0 N1 N2
  10P GAIN MUTATED    2  1  0
  10P GAIN WILD-TYPE 31 19  4
D18V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                2                 31
  N1                1                 19
  N2                0                  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 MX
  10P GAIN MUTATED    6  1  1
  10P GAIN WILD-TYPE 75  7 95
D18V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                6                 75
  M1                1                  7
  MX                1                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     3   5
  10P GAIN WILD-TYPE  55 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3    5
  10P GAIN WILD-TYPE   55  135
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                3                 55
  MALE                  5                135
[1] 2 2
[1] FALSE
D18V8, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 51 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8310 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A4ZT         TCGA-A4-A57E 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6796 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LD         TCGA-IA-A40U 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IA-A40X         TCGA-IA-A40Y         TCGA-J7-8537 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71R         TCGA-SX-A71S 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A71V         TCGA-SX-A7SL 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SN         TCGA-SX-A7SO 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SQ         TCGA-SX-A7SU 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
D18V9, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 23 
        TCGA-A4-A48D         TCGA-B1-A654         TCGA-B9-A44B 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-A69E         TCGA-G7-A8LD         TCGA-GL-7773 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-P4-A5EB         TCGA-PJ-A5Z9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71S         TCGA-SX-A71U 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-Y8-A894 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RZ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0     2
  10P GAIN WILD-TYPE                                2     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           2     2
  10P GAIN WILD-TYPE                        47   127
D18V10, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  2
  BLACK OR AFRICAN AMERICAN                       2                 47
  WHITE                                           2                127
[1] 4 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, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0   6
  10P GAIN WILD-TYPE   9 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0    6
  10P GAIN WILD-TYPE    9  147
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                6                147
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     6   0
  10Q GAIN WILD-TYPE 160   7
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 6                167 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 0                  7 
$`10Q GAIN MUTATED`
TCGA-A4-8098 TCGA-AL-3468 TCGA-B9-4617 TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-SX-A7SS 
         140         1636           35           10           36         1247 

$`10Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
           7           49            2          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 
           2          118           87            4         1778          412 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 
        1536          857          803          627           14          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1338          671           64          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         102          167           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
         771          403          233           29          364           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         419          114          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        2460         1856         1670         1040          578          757 
TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
          97            7          208         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD 
        1059          765          446          786          279         1967 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         511          608           62          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
           2            4          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         174           57         1079         1199          994          508 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SU 
         423         1973          102          925          494          847 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         224            2          186          181          205 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                  2 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1636               5925 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                88                510 
[1] "10.0 - 1636.0 (88.0)" "2.0 - 5925.0 (510.0)"
[1] "hr="     "9300000"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED         3        1         2        1
  10Q GAIN WILD-TYPE     119       10        40       11
D19V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  3                119
  STAGE II                 1                 10
  STAGE III                2                 40
  STAGE IV                 1                 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                  T1  T2 T3+T4
  10Q GAIN MUTATED     4   1     3
  10Q GAIN WILD-TYPE 126  17    47
D19V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                   4                126
  T2                   1                 17
  T3+T4                3                 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"
                    vv
clus                 N0 N1 N2
  10Q GAIN MUTATED    2  1  0
  10Q GAIN WILD-TYPE 31 19  4
D19V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                2                 31
  N1                1                 19
  N2                0                  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 MX
  10Q GAIN MUTATED    6  1  1
  10Q GAIN WILD-TYPE 75  7 95
D19V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                6                 75
  M1                1                  7
  MX                1                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3   5
  10Q GAIN WILD-TYPE  55 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    5
  10Q GAIN WILD-TYPE   55  135
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                3                 55
  MALE                  5                135
[1] 2 2
[1] FALSE
D19V8, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 51 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8310 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A4ZT         TCGA-A4-A57E 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6796 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LD         TCGA-IA-A40U 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IA-A40X         TCGA-IA-A40Y         TCGA-J7-8537 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71R         TCGA-SX-A71S 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A71V         TCGA-SX-A7SL 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SN         TCGA-SX-A7SO 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SQ         TCGA-SX-A7SU 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D19V9, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 23 
        TCGA-A4-A48D         TCGA-B1-A654         TCGA-B9-A44B 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-A69E         TCGA-G7-A8LD         TCGA-GL-7773 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-P4-A5EB         TCGA-PJ-A5Z9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71S         TCGA-SX-A71U 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-Y8-A894 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RZ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     2
  10Q GAIN WILD-TYPE                                2     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           2     2
  10Q GAIN WILD-TYPE                        47   127
D19V10, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  2
  BLACK OR AFRICAN AMERICAN                       2                 47
  WHITE                                           2                127
[1] 4 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, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0   6
  10Q GAIN WILD-TYPE   9 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    6
  10Q GAIN WILD-TYPE    9  147
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                6                147
[1] 2 2
[1] FALSE

Clustering(20) Variable = 11P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     7   0
  11P GAIN WILD-TYPE 159   7
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 7                166 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                  7 
$`11P GAIN MUTATED`
TCGA-AL-A5DJ TCGA-B9-4117 TCGA-B9-A44B TCGA-BQ-5892 TCGA-F9-A7Q0 TCGA-GL-7966 
          26           14           64          364           10          112 
TCGA-P4-A5EB 
        2584 

$`11P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
         516            2          118           87            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        1636          412          923          763         1357           67 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
         595          223          659          747          108          510 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
          14         1029          307          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
          85         1536          857          803          627           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
         460         1338          671          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         102          167           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 
         771          403          233           29           84         3760 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2948         2839         1864         1533         1516          799 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         612          232          214          218          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92         1240         2429         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
        1856         1670         1040          578          757           97 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
           7           36          208         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD 
        1059          765          446          786          279         1967 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
        5925          393          841           32          178           91 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         1726          167          511 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         608           62          677          649          146            2 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
           4          160          885          161         1043          391 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
         543          438          292           11          541          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        3035         2653         2816          391          174           57 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1079         1199          994          508          423         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 
         102          925          494         1247          847          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
           2          186          181          205 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                10                  2 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              2584               5925 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              64.0              513.5 
[1] "10.0 - 2584.0 (64.0)" "2.0 - 5925.0 (513.5)"
[1] "hr="     "2.6e+07"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED         3        0         4        2
  11P GAIN WILD-TYPE     119       11        38       10
D20V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  3                119
  STAGE II                 0                 11
  STAGE III                4                 38
  STAGE IV                 2                 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                  T1  T2 T3+T4
  11P GAIN MUTATED     3   2     5
  11P GAIN WILD-TYPE 127  16    45
D20V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                   3                127
  T2                   2                 16
  T3+T4                5                 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"
                    vv
clus                 N0 N1 N2
  11P GAIN MUTATED    2  3  0
  11P GAIN WILD-TYPE 31 17  4
D20V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0                2                 31
  N1                3                 17
  N2                0                  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 MX
  11P GAIN MUTATED    2  2  4
  11P GAIN WILD-TYPE 79  6 92
D20V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                2                 79
  M1                2                  6
  MX                4                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     5   5
  11P GAIN WILD-TYPE  53 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5    5
  11P GAIN WILD-TYPE   53  135
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                5                 53
  MALE                  5                135
[1] 2 2
[1] FALSE
D20V8, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 51 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8310 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A4ZT         TCGA-A4-A5DU 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-A5XZ         TCGA-A4-A6HP         TCGA-AL-3466 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-EV-5901 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6790 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6796         TCGA-G7-6797 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-G7-A4TM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-IA-A40U         TCGA-IA-A40X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-8537         TCGA-Q2-A5QZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A71S         TCGA-SX-A71U 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SX-A71V         TCGA-SX-A7SL         TCGA-SX-A7SM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SX-A7SN         TCGA-SX-A7SO         TCGA-SX-A7SP 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SX-A7SQ         TCGA-SX-A7SS         TCGA-SX-A7SU 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D20V9, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 22 
        TCGA-A4-A48D         TCGA-B1-A654         TCGA-B9-A69E 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-GL-7773         TCGA-GL-A59T 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-IA-A40U 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-Q2-A5QZ         TCGA-SX-A71S 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-Y8-A894         TCGA-Y8-A896 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ 
"11P GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     1
  11P GAIN WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           2     7
  11P GAIN WILD-TYPE                        47   122
D20V10, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                       2                 47
  WHITE                                           7                122
[1] 4 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, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0  10
  11P GAIN WILD-TYPE   9 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   10
  11P GAIN WILD-TYPE    9  143
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               10                143
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED     7   0
  11Q GAIN WILD-TYPE 159   7
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                166 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 0                  7 
$`11Q GAIN MUTATED`
TCGA-AL-A5DJ TCGA-B9-4117 TCGA-BQ-5892 TCGA-F9-A7Q0 TCGA-GL-7966 TCGA-P4-A5EB 
          26           14          364           10          112         2584 
TCGA-Q2-A5QZ 
          57 

$`11Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
         516            2          118           87            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        1636          412          923          763         1357           67 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
         595          223          659          747          108          510 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
          14         1029          307          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
          85         1536          857          803          627           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
           5          102          167           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 
         792          771          403          233           29           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         419          114          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        2460         1856         1670         1040          578          757 
TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
          97            7           36          208         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
        1194         1059          765          446          786          279 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        1967         5925          393          841           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         511          608           62          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
           2            4          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
         148         3035         2653         2816          391          174 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1079         1199          994          508          423         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 
         102          925          494         1247          847          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
           2          186          181          205 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                10                  2 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              2584               5925 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              57.0              513.5 
[1] "10.0 - 2584.0 (57.0)" "2.0 - 5925.0 (513.5)"
[1] "hr="     "2.6e+07"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         3        0         4        1
  11Q GAIN WILD-TYPE     119       11        38       11
D21V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  3                119
  STAGE II                 0                 11
  STAGE III                4                 38
  STAGE IV                 1                 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                  T1  T2 T3+T4
  11Q GAIN MUTATED     3   2     4
  11Q GAIN WILD-TYPE 127  16    46
D21V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                   3                127
  T2                   2                 16
  T3+T4                4                 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"
                    vv
clus                 N0 N1 N2
  11Q GAIN MUTATED    2  2  0
  11Q GAIN WILD-TYPE 31 18  4
D21V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                2                 31
  N1                2                 18
  N2                0                  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 MX
  11Q GAIN MUTATED    2  1  5
  11Q GAIN WILD-TYPE 79  7 91
D21V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                2                 79
  M1                1                  7
  MX                5                 91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     6   3
  11Q GAIN WILD-TYPE  52 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      6    3
  11Q GAIN WILD-TYPE   52  137
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                6                 52
  MALE                  3                137
[1] 2 2
[1] FALSE
D21V8, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 50 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8310 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A4ZT         TCGA-A4-A5DU 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-A5XZ         TCGA-A4-A6HP         TCGA-AL-3466 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-EV-5901 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6790 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6796         TCGA-G7-6797 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-G7-A4TM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-IA-A40U         TCGA-IA-A40X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-8537         TCGA-SX-A71R 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A71V 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-SX-A7SO         TCGA-SX-A7SP         TCGA-SX-A7SQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-SX-A7SU 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D21V9, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 22 
        TCGA-A4-A48D         TCGA-B1-A654         TCGA-B9-A44B 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B9-A69E         TCGA-G7-A8LD         TCGA-GL-7773 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-PJ-A5Z9         TCGA-SX-A71S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-Y8-A894         TCGA-Y8-A896 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ 
"11Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     1
  11Q GAIN WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           2     6
  11Q GAIN WILD-TYPE                        47   123
D21V10, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                       2                 47
  WHITE                                           6                123
[1] 4 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, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0   9
  11Q GAIN WILD-TYPE   9 144
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    9
  11Q GAIN WILD-TYPE    9  144
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                9                144
[1] 2 2
[1] FALSE

Clustering(22) Variable = 12P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   68  5
  12P GAIN WILD-TYPE 98  2
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                73                100 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 5                  2 
$`12P GAIN MUTATED`
TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 
         554          582            2          140          780           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 
         597          600          516            2            4         1636 
TCGA-AL-3471 TCGA-AL-7173 TCGA-B1-A47N TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-A6W5 
         412         1357          747           14         1029           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 
        1536          857           35         1338          671          585 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5877 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 
           5          167          270          771           29          364 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 
         232          218          116          414         1142          114 
TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-F9-A7Q0 TCGA-F9-A8NY 
         445         1240         2460         1856           10           36 
TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 
         208         1194          279         1967         5925          112 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ 
          32          178           91         2072          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         167          511           62          160          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 TCGA-MH-A854 TCGA-P4-A5EB 
        1043          391          543          292           11         2584 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SQ 
         391          174          994          508         1973          494 
TCGA-SX-A7SS 
        1247 

$`12P GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
          21          493            3           27            7           49 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         729          709          436          379          118           87 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
        1778          923          763           26           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4103 
         223          659          108          510          307          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 
        1049          379          803          627           14          460 
TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
          64          207          102           52         2639          586 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 
         403          233           84         3760         2948         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7060 
        1864         1533         1516          799          612          214 
TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7842 
         353         3950         1093          744          419           92 
TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
        2429         1670         1040          578          757           97 
TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
           7         1575         1479         1059          765          446 
TCGA-G7-7502 TCGA-GL-7773 TCGA-GL-8500 TCGA-HE-A5NH TCGA-IA-A40X TCGA-IZ-8195 
         786          393          841          408          608          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A561 TCGA-MH-A856 
         649          146            2            4          438          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-Q2-A5QZ TCGA-SX-A71R 
         148         3035         2653         2816           57         1079 
TCGA-SX-A71S TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SU TCGA-Y8-A894 
        1199          423          102          925          847          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
           2          186          181          205 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                  2 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              5925               3950 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               414                582 
[1] "2.0 - 5925.0 (414.0)" "2.0 - 3950.0 (582.0)"
[1] "hr=" "3.7"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED        53        3        12        7
  12P GAIN WILD-TYPE      69        8        30        5
D22V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                 53                 69
  STAGE II                 3                  8
  STAGE III               12                 30
  STAGE IV                 7                  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                 T1 T2 T3+T4
  12P GAIN MUTATED   56  5    20
  12P GAIN WILD-TYPE 74 13    30
D22V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                  56                 74
  T2                   5                 13
  T3+T4               20                 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                 N0 N1 N2
  12P GAIN MUTATED   11  9  2
  12P GAIN WILD-TYPE 22 11  2
D22V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               11                 22
  N1                9                 11
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  12P GAIN MUTATED   27  4 44
  12P GAIN WILD-TYPE 54  4 52
D22V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               27                 54
  M1                4                  4
  MX               44                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   16 65
  12P GAIN WILD-TYPE 42 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     16   65
  12P GAIN WILD-TYPE   42   75
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               16                 42
  MALE                 65                 75
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     2
  12P GAIN WILD-TYPE                                2     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                          22    50
  12P GAIN WILD-TYPE                        27    79
D22V10, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  2
  BLACK OR AFRICAN AMERICAN                      22                 27
  WHITE                                          50                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    1 68
  12P GAIN WILD-TYPE  8 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   68
  12P GAIN WILD-TYPE    8   85
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               68                 85
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED   68  5
  12Q GAIN WILD-TYPE 98  2
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                73                100 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                  2 
$`12Q GAIN MUTATED`
TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 
         554          582            2          140          780           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 
         597          600          516            2            4         1636 
TCGA-AL-3471 TCGA-AL-7173 TCGA-B1-A47N TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-A6W5 
         412         1357          747           14         1029           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 
        1536          857           35         1338          671          585 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5877 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 
           5          167          270          771           29          364 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 
         232          218          116          414         1142          114 
TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-F9-A7Q0 TCGA-F9-A8NY 
         445         1240         2460         1856           10           36 
TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 
         208         1194          279         1967         5925          112 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ 
          32          178           91         2072          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         167          511           62          160          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 TCGA-MH-A854 TCGA-P4-A5EB 
        1043          391          543          292           11         2584 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SQ 
         391          174          994          508         1973          494 
TCGA-SX-A7SS 
        1247 

$`12Q GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
          21          493            3           27            7           49 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         729          709          436          379          118           87 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
        1778          923          763           26           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4103 
         223          659          108          510          307          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 
        1049          379          803          627           14          460 
TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
          64          207          102           52         2639          586 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 
         403          233           84         3760         2948         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7060 
        1864         1533         1516          799          612          214 
TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7842 
         353         3950         1093          744          419           92 
TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
        2429         1670         1040          578          757           97 
TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
           7         1575         1479         1059          765          446 
TCGA-G7-7502 TCGA-GL-7773 TCGA-GL-8500 TCGA-HE-A5NH TCGA-IA-A40X TCGA-IZ-8195 
         786          393          841          408          608          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A561 TCGA-MH-A856 
         649          146            2            4          438          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-Q2-A5QZ TCGA-SX-A71R 
         148         3035         2653         2816           57         1079 
TCGA-SX-A71S TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SU TCGA-Y8-A894 
        1199          423          102          925          847          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
           2          186          181          205 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                  2 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              5925               3950 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               414                582 
[1] "2.0 - 5925.0 (414.0)" "2.0 - 3950.0 (582.0)"
[1] "hr=" "3.7"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED        53        3        12        7
  12Q GAIN WILD-TYPE      69        8        30        5
D23V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                 53                 69
  STAGE II                 3                  8
  STAGE III               12                 30
  STAGE IV                 7                  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                 T1 T2 T3+T4
  12Q GAIN MUTATED   56  5    20
  12Q GAIN WILD-TYPE 74 13    30
D23V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                  56                 74
  T2                   5                 13
  T3+T4               20                 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                 N0 N1 N2
  12Q GAIN MUTATED   11  9  2
  12Q GAIN WILD-TYPE 22 11  2
D23V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               11                 22
  N1                9                 11
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  12Q GAIN MUTATED   27  4 44
  12Q GAIN WILD-TYPE 54  4 52
D23V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               27                 54
  M1                4                  4
  MX               44                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   16 65
  12Q GAIN WILD-TYPE 42 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     16   65
  12Q GAIN WILD-TYPE   42   75
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               16                 42
  MALE                 65                 75
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     2
  12Q GAIN WILD-TYPE                                2     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                          22    50
  12Q GAIN WILD-TYPE                        27    79
D23V10, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  2
  BLACK OR AFRICAN AMERICAN                      22                 27
  WHITE                                          50                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    1 68
  12Q GAIN WILD-TYPE  8 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   68
  12Q GAIN WILD-TYPE    8   85
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               68                 85
[1] 2 2
[1] FALSE

Clustering(24) Variable = 13Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    18   1
  13Q GAIN WILD-TYPE 148   6
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                19                154 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                  6 
$`13Q GAIN MUTATED`
TCGA-A4-8311 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A5Y1 TCGA-AT-A5NU TCGA-B1-5398 
         729          600          436           87           67          595 
TCGA-B3-8121 TCGA-B9-4117 TCGA-B9-4617 TCGA-BQ-5885 TCGA-BQ-7046 TCGA-DW-5561 
         379           14           35          921         2948          414 
TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6796 TCGA-MH-A856 TCGA-P4-A5EB TCGA-SX-A7SN 
         757         1575         1059          541         2584          102 
TCGA-SX-A7SQ 
         494 

$`13Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8515 
           7           49            2          140          780          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 
          23          597          379          516            2          118 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
           4         1778         1636          412          923          763 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
        1357           26          223          659          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
         510           14         1029          307          930         1049 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5155 
          85         1536          857          803          627          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1338          671           64          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         102          167           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 
        1938         1454         1242          792          792          771 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         403          233           29          364           84         3760 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 
         232          214          218          116          353         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        1093         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
          92         1240         2429         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
        1040          578           97           10            7           36 
TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
         208         1479         1194          765          446          786 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
         279         1967         5925          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          32          178           91         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        1726          167          511          608           62          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
         649          146            2            4          160          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          391          543          438          292 
TCGA-MH-A854 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 
          11          148         3035         2653         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         174           57         1079         1199          994          508 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 
         423         1973          925         1247          847          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
           2          186          181          205 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                14                  2 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              2948               5925 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             541.0              500.5 
[1] "14.0 - 2948.0 (541.0)" "2.0 - 5925.0 (500.5)" 
[1] "hr=" "1.2"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED        15        0         5        0
  13Q GAIN WILD-TYPE     107       11        37       12
D24V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                 15                107
  STAGE II                 0                 11
  STAGE III                5                 37
  STAGE IV                 0                 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                  T1  T2 T3+T4
  13Q GAIN MUTATED    17   1     4
  13Q GAIN WILD-TYPE 113  17    46
D24V4, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                  17                113
  T2                   1                 17
  T3+T4                4                 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"
                    vv
clus                 N0 N1 N2
  13Q GAIN MUTATED    2  2  0
  13Q GAIN WILD-TYPE 31 18  4
D24V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0                2                 31
  N1                2                 18
  N2                0                  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 MX
  13Q GAIN MUTATED   10  0 11
  13Q GAIN WILD-TYPE 71  8 85
D24V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0               10                 71
  M1                0                  8
  MX               11                 85
[1] 3 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
  13Q GAIN MUTATED     6  16
  13Q GAIN WILD-TYPE  52 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      6   16
  13Q GAIN WILD-TYPE   52  124
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                6                 52
  MALE                 16                124
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                 22 
        TCGA-A4-A48D         TCGA-B1-A654         TCGA-B9-A44B 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-A69E         TCGA-G7-A8LD         TCGA-GL-7773 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-P4-A5E7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-Q2-A5QZ         TCGA-SX-A71S 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-Y8-A894         TCGA-Y8-A896 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ 
"13Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     0
  13Q GAIN WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           4    17
  13Q GAIN WILD-TYPE                        45   112
D24V10, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       4                 45
  WHITE                                          17                112
[1] 4 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, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     2  17
  13Q GAIN WILD-TYPE   7 136
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2   17
  13Q GAIN WILD-TYPE    7  136
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               17                136
[1] 2 2
[1] FALSE

Clustering(25) Variable = 14Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED     1   0
  14Q GAIN WILD-TYPE 165   7
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                172 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 0                  7 
$`14Q GAIN MUTATED`
TCGA-GL-7966 
         112 

$`14Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
         516            2          118           87            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
        1636          412          923          763         1357           26 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
          67          595          223          659          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
         510           14         1029          307          930         1049 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
         379           85         1536          857          803          627 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
          14           35          460         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
         585          207            5          102          167           52 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
        2639          586          270         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 
         792          921          792          771          403          233 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 
          29          364           84         3760         2948         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        1093         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
          92         1240         2429         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
        1040          578          757           97           10            7 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          36          208         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 
         765          446          786          279         1967         5925 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
         393          841           32          178           91         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         408          360         1726          167          511          608 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
          62          677          649          146            2            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         160          885          161         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
         438          292           11          541          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2653         2584         2816          391          174           57 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1079         1199          994          508          423         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 
         102          925          494         1247          847          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
           2          186          181          205 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               112                  2 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               112               5925 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               112                509 
[1] "112.0 - 112.0 (112.0)" "2.0 - 5925.0 (509.0)" 
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
D25V2, continuous
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                193 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7584         TCGA-A4-7585 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7732         TCGA-A4-7734         TCGA-A4-7828 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7915         TCGA-A4-7996         TCGA-A4-7997 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-8312         TCGA-A4-8515         TCGA-A4-8516 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-8517         TCGA-A4-8518         TCGA-A4-8630 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A4ZT         TCGA-A4-A57E 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A5Y0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A5Y1         TCGA-A4-A6HP         TCGA-A4-A772 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-AL-A5DJ         TCGA-AT-A5NU 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B1-A47M 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-A47N         TCGA-B1-A654         TCGA-B1-A655 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-A656         TCGA-B3-3925         TCGA-B3-3926 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B3-A6W5         TCGA-B9-4113         TCGA-B9-4114 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-A5W8         TCGA-B9-A5W9         TCGA-B9-A69E 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-A8YH         TCGA-B9-A8YI         TCGA-BQ-5875 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5881         TCGA-BQ-5882 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-F9-A4JJ         TCGA-F9-A7Q0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F9-A7VF         TCGA-F9-A8NY         TCGA-G7-6789 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-G7-A4TM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-GL-6846         TCGA-GL-7773 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-HE-A5NF         TCGA-HE-A5NH 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-HE-A5NL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40X         TCGA-IA-A40Y 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IZ-8195         TCGA-IZ-8196         TCGA-IZ-A6M8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IZ-A6M9         TCGA-J7-6720         TCGA-J7-8537 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KV-A6GD         TCGA-KV-A6GE         TCGA-KV-A74V 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A55W         TCGA-MH-A55Z         TCGA-MH-A560 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A561         TCGA-MH-A562         TCGA-MH-A854 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A856         TCGA-O9-A75Z         TCGA-P4-A5E6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-P4-A5E8         TCGA-P4-A5EA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-P4-A5ED         TCGA-PJ-A5Z8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-Q2-A5QZ         TCGA-SX-A71R 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A71V 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SN 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SO         TCGA-SX-A7SP         TCGA-SX-A7SQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-SX-A7SU         TCGA-Y8-A894 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A895         TCGA-Y8-A896         TCGA-Y8-A898 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ 
"14Q GAIN WILD-TYPE" 
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q GAIN MUTATED         0        0         3        0
  14Q GAIN WILD-TYPE     122       11        39       12
D25V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  0                122
  STAGE II                 0                 11
  STAGE III                3                 39
  STAGE IV                 0                 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                  T1  T2 T3+T4
  14Q GAIN MUTATED     0   0     3
  14Q GAIN WILD-TYPE 130  18    47
D25V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                   0                130
  T2                   0                 18
  T3+T4                3                 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"
                    vv
clus                 N0 N1 N2
  14Q GAIN MUTATED    0  2  0
  14Q GAIN WILD-TYPE 33 18  4
D25V5, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                 55 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y1         TCGA-AL-3466 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-A655         TCGA-B1-A656 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5877         TCGA-BQ-5878 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5882         TCGA-BQ-5885 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7045 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7050         TCGA-BQ-7051 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-DW-7963 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-F9-A8NY         TCGA-G7-6789 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-7501 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-GL-6846         TCGA-GL-A59R 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40Y         TCGA-J7-6720 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-J7-8537         TCGA-KV-A74V         TCGA-P4-A5E6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P4-A5E8         TCGA-P4-A5EA         TCGA-SX-A71R 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SP         TCGA-SX-A7SS 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ 
"14Q GAIN WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  14Q GAIN MUTATED    2  0  1
  14Q GAIN WILD-TYPE 79  8 95
D25V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                2                 79
  M1                0                  8
  MX                1                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2   1
  14Q GAIN WILD-TYPE  56 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2    1
  14Q GAIN WILD-TYPE   56  139
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                2                 56
  MALE                  1                139
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     0
  14Q GAIN WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           0     2
  14Q GAIN WILD-TYPE                        49   127
D25V10, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                182 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7584         TCGA-A4-7585 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7732         TCGA-A4-7734         TCGA-A4-7828 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7915         TCGA-A4-7996         TCGA-A4-7997 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-8312         TCGA-A4-8515         TCGA-A4-8516 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-8517         TCGA-A4-8518         TCGA-A4-8630 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A4ZT         TCGA-A4-A57E 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A5Y0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A5Y1         TCGA-A4-A6HP         TCGA-A4-A772 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-AL-A5DJ         TCGA-AT-A5NU 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B1-A47M 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-A47N         TCGA-B1-A654         TCGA-B1-A655 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-A656         TCGA-B3-3925         TCGA-B3-3926 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B3-A6W5         TCGA-B9-4113         TCGA-B9-4114 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-A5W8         TCGA-B9-A5W9         TCGA-B9-A69E 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B9-A8YH         TCGA-B9-A8YI         TCGA-BQ-5875 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5881         TCGA-BQ-5883 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-7044         TCGA-BQ-7045 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6133         TCGA-DZ-6134 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F9-A4JJ         TCGA-F9-A7Q0         TCGA-F9-A7VF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F9-A8NY         TCGA-G7-6789         TCGA-G7-6790 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-G7-A4TM         TCGA-G7-A8LD 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7773         TCGA-GL-8500 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-A4EM         TCGA-GL-A59R         TCGA-GL-A59T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40X         TCGA-IA-A40Y 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IZ-8195         TCGA-IZ-8196         TCGA-IZ-A6M8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IZ-A6M9         TCGA-J7-6720         TCGA-J7-8537 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KV-A6GD         TCGA-KV-A6GE         TCGA-KV-A74V 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A55W         TCGA-MH-A55Z         TCGA-MH-A560 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A561         TCGA-MH-A562         TCGA-MH-A854 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A856         TCGA-O9-A75Z         TCGA-P4-A5E6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-P4-A5E8         TCGA-P4-A5EA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-P4-A5ED         TCGA-PJ-A5Z8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-Q2-A5QZ         TCGA-SX-A71R 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A71V 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SN         TCGA-SX-A7SO 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SQ         TCGA-SX-A7SS 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A895         TCGA-Y8-A896 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A898         TCGA-Y8-A8RZ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
D25V11, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0   1
  14Q GAIN WILD-TYPE   9 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0    1
  14Q GAIN WILD-TYPE    9  152
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                1                152
[1] 2 2
[1] FALSE

Clustering(26) Variable = 15Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED     5   0
  15Q GAIN WILD-TYPE 161   7
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                168 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 0                  7 
$`15Q GAIN MUTATED`
TCGA-AL-A5DJ TCGA-B1-7332 TCGA-BQ-5892 TCGA-P4-A5EB TCGA-Q2-A5QZ 
          26          223          364         2584           57 

$`15Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
         516            2          118           87            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        1636          412          923          763         1357           67 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         595          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
           5          102          167           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 
         792          771          403          233           29           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         419          114          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        2460         1856         1670         1040          578          757 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 
          97           10            7           36          208         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
        1479         1194         1059          765          446          786 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
         279         1967         5925          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          32          178           91         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        1726          167          511          608           62          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
         649          146            2            4          160          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          391          543          438          292 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED 
          11          541          148         3035         2653         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         391          174         1079         1199          994          508 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS 
         423         1973          102          925          494         1247 
TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         847          224            2          186          181          205 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                26                  2 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              2584               5925 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             223.0              510.5 
[1] "26.0 - 2584.0 (223.0)" "2.0 - 5925.0 (510.5)" 
[1] "hr="     "2.6e+07"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED         2        1         2        0
  15Q GAIN WILD-TYPE     120       10        40       12
D26V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  2                120
  STAGE II                 1                 10
  STAGE III                2                 40
  STAGE IV                 0                 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                  T1  T2 T3+T4
  15Q GAIN MUTATED     2   1     2
  15Q GAIN WILD-TYPE 128  17    48
D26V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                   2                128
  T2                   1                 17
  T3+T4                2                 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"
                    vv
clus                 N0 N1 N2
  15Q GAIN MUTATED    1  0  0
  15Q GAIN WILD-TYPE 32 20  4
D26V5, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 56 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y1         TCGA-AL-3466 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-A655         TCGA-B1-A656 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5877         TCGA-BQ-5878 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5882 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5887         TCGA-BQ-5888 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7045 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7050         TCGA-BQ-7051 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-DW-7963 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-F9-A8NY         TCGA-G7-6789 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-7501 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-GL-6846         TCGA-GL-7966 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GL-A59R         TCGA-IA-A40U         TCGA-IA-A40Y 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537         TCGA-KV-A74V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-A5E8         TCGA-P4-A5EA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A7SM         TCGA-SX-A7SP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-Y8-A8RZ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  15Q GAIN MUTATED    1  0  4
  15Q GAIN WILD-TYPE 80  8 92
D26V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                1                 80
  M1                0                  8
  MX                4                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     3   2
  15Q GAIN WILD-TYPE  55 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    2
  15Q GAIN WILD-TYPE   55  138
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                3                 55
  MALE                  2                138
[1] 2 2
[1] FALSE
D26V8, continuous
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 51 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8310 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A4ZT         TCGA-A4-A57E 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6796 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LD         TCGA-IA-A40U 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IA-A40X         TCGA-IA-A40Y         TCGA-J7-8537 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A71S         TCGA-SX-A71U 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A71V         TCGA-SX-A7SL         TCGA-SX-A7SM 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A7SN         TCGA-SX-A7SO         TCGA-SX-A7SP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A7SQ         TCGA-SX-A7SS         TCGA-SX-A7SU 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D26V9, continuous
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 22 
        TCGA-A4-A48D         TCGA-B1-A654         TCGA-B9-A44B 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B9-A69E         TCGA-G7-A8LD         TCGA-GL-7773 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-PJ-A5Z9         TCGA-SX-A71S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-Y8-A894         TCGA-Y8-A896 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ 
"15Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     0
  15Q GAIN WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           2     3
  15Q GAIN WILD-TYPE                        47   126
D26V10, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       2                 47
  WHITE                                           3                126
[1] 4 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, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0   5
  15Q GAIN WILD-TYPE   9 148
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    5
  15Q GAIN WILD-TYPE    9  148
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                5                148
[1] 2 2
[1] FALSE

Clustering(27) Variable = 16P GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED   89  2
  16P GAIN WILD-TYPE 77  5
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                91                 82 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                  5 
$`16P GAIN MUTATED`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 
         554          493            3           49            2          780 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
         729          709           23          597          600          436 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-3471 
         379          516            2           87         1636          412 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 
          67          595          659          930          379           85 
TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         857           14           35          460         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5881 
          64          585            5           52         2639         1454 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7046 
         792          771          233           29         3760         2948 
TCGA-BQ-7051 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 
        1533          214          116         3950         1093          744 
TCGA-DW-7963 TCGA-DZ-6134 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF 
        1240         1856          578          757           10            7 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6797 TCGA-GL-6846 TCGA-GL-7966 
          36          208         1575          765         5925          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ 
         841           32           91         2072          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         167          511           62          677          146            2 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A560 TCGA-MH-A854 
         160          885          161         1043          543           11 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71U 
        3035         2653         2584          174         1079          994 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-Y8-A895 
         508          423          102          494         1247            2 
TCGA-Y8-A898 
         181 

$`16P GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-A5Y0 
          21          582           27            7          140          118 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
           4         1778          923          763         1357           26 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         223          747          108          510           14         1029 
TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A5W8 
         307         1049         1536          803          627          207 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5883 
         102          167          586          270         1938         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7048 
         792          921          403          364           84         2839 
TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 
        1864         1516          799          612          232          218 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
         353          414         1142          419          114          445 
TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-F9-A4JJ 
          92         2429         2460         1670         1040           97 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
        1479         1194         1059          446          786          279 
TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-A59R TCGA-HE-A5NH TCGA-IA-A40X TCGA-IZ-8196 
        1967          393          178          408          608          649 
TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A856 TCGA-O9-A75Z 
           4          391          438          292          541          148 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71S TCGA-SX-A7SM TCGA-SX-A7SO 
        2816          391           57         1199         1973          925 
TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8RZ 
         847          224          186          205 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                  4 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              5925               2839 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             511.0              445.5 
[1] "2.0 - 5925.0 (511.0)" "4.0 - 2839.0 (445.5)"
[1] "hr=" "2.9"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED        66        5        23        5
  16P GAIN WILD-TYPE      56        6        19        7
D27V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                 66                 56
  STAGE II                 5                  6
  STAGE III               23                 19
  STAGE IV                 5                  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                 T1 T2 T3+T4
  16P GAIN MUTATED   72 10    24
  16P GAIN WILD-TYPE 58  8    26
D27V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                  72                 58
  T2                  10                  8
  T3+T4               24                 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                 N0 N1 N2
  16P GAIN MUTATED   16 10  2
  16P GAIN WILD-TYPE 17 10  2
D27V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               16                 17
  N1               10                 10
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  16P GAIN MUTATED   41  3 54
  16P GAIN WILD-TYPE 40  5 42
D27V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0               41                 40
  M1                3                  5
  MX               54                 42
[1] 3 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
  16P GAIN MUTATED   22 84
  16P GAIN WILD-TYPE 36 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     22   84
  16P GAIN WILD-TYPE   36   56
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               22                 36
  MALE                 84                 56
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  2     2
  16P GAIN WILD-TYPE                                0     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                          19    76
  16P GAIN WILD-TYPE                        30    53
D27V10, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           2                  2
  BLACK OR AFRICAN AMERICAN                      19                 30
  WHITE                                          76                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    2 85
  16P GAIN WILD-TYPE  7 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2   85
  16P GAIN WILD-TYPE    7   68
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               85                 68
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16Q GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   88  1
  16Q GAIN WILD-TYPE 78  6
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                89                 84 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                  6 
$`16Q GAIN MUTATED`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 
         554          493            3           49            2          780 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
         729          709           23          597          600          436 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU 
         379          516            2         1636          412           67 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4114 
         595          659          930          379           85          857 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
          14           35          460         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5881 TCGA-BQ-5886 
         585            5           52         2639         1454          792 
TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7060 
         771           29         3760         2948         1533          214 
TCGA-BQ-7062 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6134 
         116         3950         1093          744         1240         1856 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 
         578          757           10            7           36          208 
TCGA-G7-6790 TCGA-G7-6797 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        1575          765         5925          112          841           32 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
          91         2072          360          167          511          608 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
          62          677          146            2          160          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A560 TCGA-MH-A854 TCGA-P4-A5E6 TCGA-P4-A5E7 
         161         1043          543           11         3035         2653 
TCGA-P4-A5EB TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
        2584          174         1079          994          508          423 
TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-Y8-A895 TCGA-Y8-A898 
         102          494         1247            2          181 

$`16Q GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-A5Y0 
          21          582           27            7          140          118 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
          87            4         1778          923          763         1357 
TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
          26          223          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 
        1029          307         1049         1536          803          627 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
         207          102          167          586          270         1938 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5892 
        1242          792          921          403          233          364 
TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
          84         2839         1864         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 
         232          218          353          414         1142          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 
         114          445           92         2429         2460         1670 
TCGA-EV-5901 TCGA-F9-A4JJ TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 
        1040           97         1479         1194         1059          446 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-A59R TCGA-HE-A5NH 
         786          279         1967          393          178          408 
TCGA-HE-A5NJ TCGA-IZ-8196 TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 
        1726          649            4          391          438          292 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71S 
         541          148         2816          391           57         1199 
TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8RZ 
        1973          925          847          224          186          205 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                  4 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              5925               2839 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             516.0              441.5 
[1] "2.0 - 5925.0 (516.0)" "4.0 - 2839.0 (441.5)"
[1] "hr=" "6.8"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED        67        5        20        4
  16Q GAIN WILD-TYPE      55        6        22        8
D28V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                 67                 55
  STAGE II                 5                  6
  STAGE III               20                 22
  STAGE IV                 4                  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                 T1 T2 T3+T4
  16Q GAIN MUTATED   71 10    21
  16Q GAIN WILD-TYPE 59  8    29
D28V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                  71                 59
  T2                  10                  8
  T3+T4               21                 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                 N0 N1 N2
  16Q GAIN MUTATED   15  8  1
  16Q GAIN WILD-TYPE 18 12  3
D28V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               15                 18
  N1                8                 12
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  16Q GAIN MUTATED   38  2 54
  16Q GAIN WILD-TYPE 43  6 42
D28V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0               38                 43
  M1                2                  6
  MX               54                 42
[1] 3 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
  16Q GAIN MUTATED   23 79
  16Q GAIN WILD-TYPE 35 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     23   79
  16Q GAIN WILD-TYPE   35   61
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               23                 35
  MALE                 79                 61
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  2     2
  16Q GAIN WILD-TYPE                                0     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                          20    72
  16Q GAIN WILD-TYPE                        29    57
D28V10, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           2                  2
  BLACK OR AFRICAN AMERICAN                      20                 29
  WHITE                                          72                 57
[1] 4 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, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    2 82
  16Q GAIN WILD-TYPE  7 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2   82
  16Q GAIN WILD-TYPE    7   71
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               82                 71
[1] 2 2
[1] FALSE

Clustering(29) Variable = 17P GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED   107   2
  17P GAIN WILD-TYPE  59   5
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               109                 64 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                  5 
$`17P GAIN MUTATED`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-8310 
         554          493          582           27           49          780 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
         729          709           23          597          600          436 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 
         516            2          118            4         1636          412 
TCGA-AL-3472 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
         923           26           67          223          659          747 
TCGA-B1-A654 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
         108         1029          930          379           85         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         857          803           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5887 
         671          585            5          167         1454          771 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7060 TCGA-BQ-7062 
          29          364         2948         1533          214          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6134 
         419          114          445           92         1240         1856 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 
        1040          757           10            7           36         1575 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 
        1194         1059          786          279         1967         5925 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
         112           32          178           91         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
         360          167          511           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         146            2            4          160          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-O9-A75Z 
        1043          391          543          438          292          148 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2653         2584          174         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A895 
         508          102          494         1247          847            2 
TCGA-Y8-A898 
         181 

$`17P GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7915 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-A48D 
          21            3            7            2          140          379 
TCGA-A4-A5Y1 TCGA-AL-3467 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A655 
          87         1778          763         1357          595          510 
TCGA-B1-A656 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W8 
          14          307         1049          627           64          207 
TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
         102           52         2639          586          270         1938 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 
        1242          792          921          792          403          233 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 
          84         3760         2839         1864         1516          799 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 
         612          232          218         2429         2460         1670 
TCGA-EV-5902 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6797 TCGA-G7-7501 
         578           97          208         1479          765          446 
TCGA-GL-7773 TCGA-GL-8500 TCGA-HE-A5NJ TCGA-IA-A40X TCGA-MH-A854 TCGA-MH-A856 
         393          841         1726          608           11          541 
TCGA-P4-A5E6 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A7SL TCGA-SX-A7SM 
        3035         2816          391           57          423         1973 
TCGA-SX-A7SO TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8RZ 
         925          224          186          205 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                  2 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              5925               3760 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             493.0              559.5 
[1] "2.0 - 5925.0 (493.0)" "2.0 - 3760.0 (559.5)"
[1] "hr=" "3.1"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P GAIN MUTATED        88        6        15        3
  17P GAIN WILD-TYPE      34        5        27        9
D29V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                 88                 34
  STAGE II                 6                  5
  STAGE III               15                 27
  STAGE IV                 3                  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                 T1 T2 T3+T4
  17P GAIN MUTATED   90 11    19
  17P GAIN WILD-TYPE 40  7    31
D29V4, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                  90                 40
  T2                  11                  7
  T3+T4               19                 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                 N0 N1 N2
  17P GAIN MUTATED   16  8  0
  17P GAIN WILD-TYPE 17 12  4
D29V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               16                 17
  N1                8                 12
  N2                0                  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 MX
  17P GAIN MUTATED   38  2 70
  17P GAIN WILD-TYPE 43  6 26
D29V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0               38                 43
  M1                2                  6
  MX               70                 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"
D29V7, binary
                    cls
clus                  0  1
  17P GAIN MUTATED   29 91
  17P GAIN WILD-TYPE 29 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     29   91
  17P GAIN WILD-TYPE   29   49
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               29                 29
  MALE                 91                 49
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  2     4
  17P GAIN WILD-TYPE                                0     0
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                          27    80
  17P GAIN WILD-TYPE                        22    49
D29V10, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           4                  0
  BLACK OR AFRICAN AMERICAN                      27                 22
  WHITE                                          80                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     4 102
  17P GAIN WILD-TYPE   5  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4  102
  17P GAIN WILD-TYPE    5   51
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO              102                 51
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17Q GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED   117   3
  17Q GAIN WILD-TYPE  49   4
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               120                 53 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                  4 
$`17Q GAIN MUTATED`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
         554          493          582           27            7           49 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
         780          729          709           23          597          600 
TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3468 
         436          516            2          118            4         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M 
         412          923           26           67          223          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 
         747          108          510         1029          930          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
          85         1536          857          803           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 
         460         1338          671           64          585            5 
TCGA-B9-A8YH TCGA-BQ-5875 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
         167         2639         1454          792          771          403 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7053 
         233           29          364         2948         1533         1516 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         214          116          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 
        1240         2460         1856         1040          757           10 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-6796 
           7           36          208         1575         1194         1059 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM 
         786          279         1967         5925          112           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NL 
         178           91         2072          408          360          167 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         511           62          677          649          146            2 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
           4          160          885          161         1043          391 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EB 
         543          438          292          148         2653         2584 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         174           57         1079         1199          994          508 
TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A895 TCGA-Y8-A898 
         102          494         1247          847            2          181 

$`17Q GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-A48D TCGA-A4-A5Y1 
          21            3            2          140          379           87 
TCGA-AL-3467 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A656 TCGA-B3-3926 
        1778          763         1357          595           14          307 
TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5876 
        1049          627          207          102           52          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5894 
         270         1938         1242          792          921           84 
TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        3760         2839         1864          799          612          232 
TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-G7-6792 
         218         2429         1670          578           97         1479 
TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-7773 TCGA-GL-8500 TCGA-HE-A5NJ TCGA-IA-A40X 
         765          446          393          841         1726          608 
TCGA-MH-A854 TCGA-MH-A856 TCGA-P4-A5E6 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-SX-A7SL 
          11          541         3035         2816          391          423 
TCGA-SX-A7SM TCGA-SX-A7SO TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8RZ 
        1973          925          224          186          205 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                  2 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              5925               3760 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             476.5              586.0 
[1] "2.0 - 5925.0 (476.5)" "2.0 - 3760.0 (586.0)"
[1] "hr=" "2.3"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED        91        7        22        7
  17Q GAIN WILD-TYPE      31        4        20        5
D30V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                 91                 31
  STAGE II                 7                  4
  STAGE III               22                 20
  STAGE IV                 7                  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                 T1 T2 T3+T4
  17Q GAIN MUTATED   93 13    29
  17Q GAIN WILD-TYPE 37  5    21
D30V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                  93                 37
  T2                  13                  5
  T3+T4               29                 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                 N0 N1 N2
  17Q GAIN MUTATED   21  9  3
  17Q GAIN WILD-TYPE 12 11  1
D30V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               21                 12
  N1                9                 11
  N2                3                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  17Q GAIN MUTATED   45  4 75
  17Q GAIN WILD-TYPE 36  4 21
D30V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               45                 36
  M1                4                  4
  MX               75                 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"
D30V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   37 98
  17Q GAIN WILD-TYPE 21 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     37   98
  17Q GAIN WILD-TYPE   21   42
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               37                 21
  MALE                 98                 42
[1] 2 2
[1] FALSE
D30V8, continuous
D30V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  2     4
  17Q GAIN WILD-TYPE                                0     0
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                          31    90
  17Q GAIN WILD-TYPE                        18    39
D30V10, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           4                  0
  BLACK OR AFRICAN AMERICAN                      31                 18
  WHITE                                          90                 39
[1] 4 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, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     5 112
  17Q GAIN WILD-TYPE   4  41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5  112
  17Q GAIN WILD-TYPE    4   41
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                  4
  NOT HISPANIC OR LATINO              112                 41
[1] 2 2
[1] FALSE

Clustering(31) Variable = 18P GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED     7   1
  18P GAIN WILD-TYPE 159   6
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 8                165 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 1                  6 
$`18P GAIN MUTATED`
TCGA-A4-A5Y1 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-5155 TCGA-DW-5560 TCGA-G7-6790 
          87          930         1049          460          353         1575 
TCGA-HE-A5NJ TCGA-SX-A7SS 
        1726         1247 

$`18P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
         516            2          118            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
         412          923          763         1357           26           67 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
         595          223          659          747          108          510 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
          14         1029          307          379           85         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
         857          803          627           14           35         1338 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
         671           64          585          207            5          102 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
         167           52         2639          586          270         1938 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
        1454         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         403          233           29          364           84         3760 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2948         2839         1864         1533         1516          799 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 
         612          232          214          218          116          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
         445           92         1240         2429         2460         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
        1670         1040          578          757           97           10 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
           7           36          208         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 
         765          446          786          279         1967         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          178           91 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
        2072          408          360          167          511          608 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
          62          677          649          146            2            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         160          885          161         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
         438          292           11          541          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2653         2584         2816          391          174           57 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1079         1199          994          508          423         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 
         102          925          494          847          224            2 
TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         186          181          205 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                87                  2 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              1726               5925 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             989.5              494.0 
[1] "87.0 - 1726.0 (989.5)" "2.0 - 5925.0 (494.0)" 
[1] "hr=" "3.8"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P GAIN MUTATED         4        1         2        1
  18P GAIN WILD-TYPE     118       10        40       11
D31V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  4                118
  STAGE II                 1                 10
  STAGE III                2                 40
  STAGE IV                 1                 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                  T1  T2 T3+T4
  18P GAIN MUTATED     6   1     2
  18P GAIN WILD-TYPE 124  17    48
D31V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                   6                124
  T2                   1                 17
  T3+T4                2                 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"
                    vv
clus                 N0 N1 N2
  18P GAIN MUTATED    1  2  0
  18P GAIN WILD-TYPE 32 18  4
D31V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                1                 32
  N1                2                 18
  N2                0                  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 MX
  18P GAIN MUTATED    5  1  2
  18P GAIN WILD-TYPE 76  7 94
D31V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                5                 76
  M1                1                  7
  MX                2                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     1   8
  18P GAIN WILD-TYPE  57 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    8
  18P GAIN WILD-TYPE   57  132
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                1                 57
  MALE                  8                132
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 22 
        TCGA-A4-A48D         TCGA-B1-A654         TCGA-B9-A44B 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-A69E         TCGA-G7-A8LD         TCGA-GL-7773 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-HE-A5NI         TCGA-IA-A40U 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-PJ-A5Z9         TCGA-Q2-A5QZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-Y8-A894         TCGA-Y8-A896 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ 
"18P GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     0
  18P GAIN WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           0     8
  18P GAIN WILD-TYPE                        49   121
D31V10, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                 49
  WHITE                                           8                121
[1] 4 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, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0   8
  18P GAIN WILD-TYPE   9 145
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0    8
  18P GAIN WILD-TYPE    9  145
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                8                145
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18Q GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED     6   0
  18Q GAIN WILD-TYPE 160   7
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                167 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                  7 
$`18Q GAIN MUTATED`
TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-5155 TCGA-DW-5560 TCGA-G7-6790 TCGA-SX-A7SS 
         930         1049          460          353         1575         1247 

$`18Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
         516            2          118           87            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
        1636          412          923          763         1357           26 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
          67          595          223          659          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-8121 TCGA-B3-A6W5 
         510           14         1029          307          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1338          671           64          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         102          167           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
         771          403          233           29          364           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          232          214          218          116 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92         1240         2429         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
        1856         1670         1040          578          757           97 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6795 
          10            7           36          208         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD 
        1059          765          446          786          279         1967 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         511          608           62          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
           2            4          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         174           57         1079         1199          994          508 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SU 
         423         1973          102          925          494          847 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         224            2          186          181          205 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               353                  2 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              1575               5925 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             989.5              494.0 
[1] "353.0 - 1575.0 (989.5)" "2.0 - 5925.0 (494.0)"  
[1] "hr="     "2.6e+07"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED         4        1         1        0
  18Q GAIN WILD-TYPE     118       10        41       12
D32V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  4                118
  STAGE II                 1                 10
  STAGE III                1                 41
  STAGE IV                 0                 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                  T1  T2 T3+T4
  18Q GAIN MUTATED     4   1     1
  18Q GAIN WILD-TYPE 126  17    49
D32V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                   4                126
  T2                   1                 17
  T3+T4                1                 49
[1] 3 2
[1] 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  0  0
  18Q GAIN WILD-TYPE 32 20  4
D32V5, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 56 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y1         TCGA-AL-3466 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-A655         TCGA-B1-A656 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5877         TCGA-BQ-5878 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5882 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5887         TCGA-BQ-5888 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7048         TCGA-BQ-7050 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7056         TCGA-BQ-7058 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7963         TCGA-DZ-6131         TCGA-F9-A8NY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6793         TCGA-G7-6795 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LD         TCGA-GL-6846 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GL-7966         TCGA-GL-A59R         TCGA-IA-A40U 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-6720         TCGA-J7-8537 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-KV-A74V         TCGA-P4-A5E6         TCGA-P4-A5E8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-P4-A5EA         TCGA-SX-A71R         TCGA-SX-A7SM 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-Y8-A8RZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  18Q GAIN MUTATED    4  0  1
  18Q GAIN WILD-TYPE 77  8 95
D32V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                4                 77
  M1                0                  8
  MX                1                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1   5
  18Q GAIN WILD-TYPE  57 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    5
  18Q GAIN WILD-TYPE   57  135
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                 57
  MALE                  5                135
[1] 2 2
[1] FALSE
D32V8, continuous
D32V9, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 23 
        TCGA-A4-A48D         TCGA-B1-A654         TCGA-B9-A44B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-A69E         TCGA-G7-A8LD         TCGA-GL-7773 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-P4-A5EB         TCGA-PJ-A5Z9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71S         TCGA-SX-A71U 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-Y8-A894 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     0
  18Q GAIN WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           0     6
  18Q GAIN WILD-TYPE                        49   123
D32V10, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                 49
  WHITE                                           6                123
[1] 4 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, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0   6
  18Q GAIN WILD-TYPE   9 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    6
  18Q GAIN WILD-TYPE    9  147
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                6                147
[1] 2 2
[1] FALSE

Clustering(33) Variable = 19P GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED     4   0
  19P GAIN WILD-TYPE 162   7
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                169 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 0                  7 
$`19P GAIN MUTATED`
TCGA-BQ-5885 TCGA-BQ-5892 TCGA-F9-A7Q0 TCGA-GL-7966 
         921          364           10          112 

$`19P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
         516            2          118           87            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
        1636          412          923          763         1357           26 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
          67          595          223          659          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
         510           14         1029          307          930         1049 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
         379           85         1536          857          803          627 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
          14           35          460         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
         585          207            5          102          167           52 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
        2639          586          270         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
         792          792          771          403          233           29 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
          84         3760         2948         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1516          799          612          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         116          353          414         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        2429         2460         1856         1670         1040          578 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 
         757           97            7           36          208         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
        1479         1194         1059          765          446          786 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
         279         1967         5925          393          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
         167          511          608           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         146            2            4          160          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          391          543          438          292           11 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         541          148         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
         391          174           57         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         508          423         1973          102          925          494 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
        1247          847          224            2          186          181 
TCGA-Y8-A8RZ 
         205 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                10                  2 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               921               5925 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               238                510 
[1] "10.0 - 921.0 (238.0)" "2.0 - 5925.0 (510.0)"
[1] "hr="     "9200000"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P GAIN MUTATED         2        0         2        0
  19P GAIN WILD-TYPE     120       11        40       12
D33V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  2                120
  STAGE II                 0                 11
  STAGE III                2                 40
  STAGE IV                 0                 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                  T1  T2 T3+T4
  19P GAIN MUTATED     2   0     2
  19P GAIN WILD-TYPE 128  18    48
D33V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                   2                128
  T2                   0                 18
  T3+T4                2                 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"
                    vv
clus                 N0 N1 N2
  19P GAIN MUTATED    2  1  0
  19P GAIN WILD-TYPE 31 19  4
D33V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                2                 31
  N1                1                 19
  N2                0                  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 MX
  19P GAIN MUTATED    3  0  1
  19P GAIN WILD-TYPE 78  8 95
D33V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                3                 78
  M1                0                  8
  MX                1                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     2   2
  19P GAIN WILD-TYPE  56 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2    2
  19P GAIN WILD-TYPE   56  138
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                2                 56
  MALE                  2                138
[1] 2 2
[1] FALSE
D33V8, continuous
D33V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     1
  19P GAIN WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           0     3
  19P GAIN WILD-TYPE                        49   126
D33V10, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                       0                 49
  WHITE                                           3                126
[1] 4 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, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0   4
  19P GAIN WILD-TYPE   9 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    4
  19P GAIN WILD-TYPE    9  149
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                4                149
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19Q GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED     4   0
  19Q GAIN WILD-TYPE 162   7
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                169 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                  7 
$`19Q GAIN MUTATED`
TCGA-BQ-5885 TCGA-BQ-5892 TCGA-F9-A7Q0 TCGA-GL-7966 
         921          364           10          112 

$`19Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
         516            2          118           87            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
        1636          412          923          763         1357           26 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
          67          595          223          659          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
         510           14         1029          307          930         1049 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
         379           85         1536          857          803          627 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
          14           35          460         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
         585          207            5          102          167           52 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
        2639          586          270         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
         792          792          771          403          233           29 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
          84         3760         2948         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1516          799          612          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         116          353          414         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        2429         2460         1856         1670         1040          578 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 
         757           97            7           36          208         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
        1479         1194         1059          765          446          786 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
         279         1967         5925          393          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
         167          511          608           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         146            2            4          160          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          391          543          438          292           11 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         541          148         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
         391          174           57         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         508          423         1973          102          925          494 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
        1247          847          224            2          186          181 
TCGA-Y8-A8RZ 
         205 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                10                  2 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               921               5925 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               238                510 
[1] "10.0 - 921.0 (238.0)" "2.0 - 5925.0 (510.0)"
[1] "hr="     "9200000"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED         2        0         2        0
  19Q GAIN WILD-TYPE     120       11        40       12
D34V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  2                120
  STAGE II                 0                 11
  STAGE III                2                 40
  STAGE IV                 0                 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                  T1  T2 T3+T4
  19Q GAIN MUTATED     2   0     2
  19Q GAIN WILD-TYPE 128  18    48
D34V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                   2                128
  T2                   0                 18
  T3+T4                2                 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"
                    vv
clus                 N0 N1 N2
  19Q GAIN MUTATED    2  1  0
  19Q GAIN WILD-TYPE 31 19  4
D34V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                2                 31
  N1                1                 19
  N2                0                  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 MX
  19Q GAIN MUTATED    3  0  1
  19Q GAIN WILD-TYPE 78  8 95
D34V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0                3                 78
  M1                0                  8
  MX                1                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     2   2
  19Q GAIN WILD-TYPE  56 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    2
  19Q GAIN WILD-TYPE   56  138
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                2                 56
  MALE                  2                138
[1] 2 2
[1] FALSE
D34V8, continuous
D34V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     1
  19Q GAIN WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           0     3
  19Q GAIN WILD-TYPE                        49   126
D34V10, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                       0                 49
  WHITE                                           3                126
[1] 4 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, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     0   4
  19Q GAIN WILD-TYPE   9 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0    4
  19Q GAIN WILD-TYPE    9  149
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                4                149
[1] 2 2
[1] FALSE

Clustering(35) Variable = 20P GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    59   2
  20P GAIN WILD-TYPE 107   5
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                61                112 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                  5 
$`20P GAIN MUTATED`
TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 
         554          582           27           49            2          780 
TCGA-A4-8311 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A5XZ TCGA-A4-A5Y1 TCGA-AL-3468 
         729          597          600            2           87         1636 
TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-3925 
         412           67          223          747          108         1029 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-7268 TCGA-B9-A5W9 
         930          379           14           35          671            5 
TCGA-B9-A8YH TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7046 
         167          771           29          364           84         2948 
TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7841 
        1533          116          353          414         1093          445 
TCGA-DZ-6132 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6789 TCGA-G7-6795 
        2460          578           10            7          208         1194 
TCGA-G7-6797 TCGA-GL-7966 TCGA-HE-A5NF TCGA-HE-A5NI TCGA-IA-A40Y TCGA-IZ-8195 
         765          112         2072          360           62          677 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A562 TCGA-MH-A854 TCGA-PJ-A5Z9 
         160          885         1043          292           11          174 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SQ TCGA-SX-A7SS 
          57         1079          508          423          494         1247 
TCGA-Y8-A895 
           2 

$`20P GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8515 
          21          493            3            7          140          709 
TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5Y0 TCGA-A4-A6HP 
          23          436          379          516          118            4 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 
        1778          923          763         1357           26          595 
TCGA-B1-A47M TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-A6W5 
         659          510           14          307         1049           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5155 TCGA-B9-5156 
        1536          857          803          627          460         1338 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 
          64          585          207          102           52         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
         586          270         1938         1454         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-7044 TCGA-BQ-7048 
         921          792          403          233         3760         2839 
TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1864         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
         218         3950         1142          744          419          114 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
          92         1240         2429         1856         1670         1040 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6796 
         757           97           36         1575         1479         1059 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 
         446          786          279         1967         5925          393 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NH TCGA-HE-A5NJ 
         841           32          178           91          408         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         167          511          608          649          146            2 
TCGA-J7-8537 TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A856 
           4          161          391          543          438          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SU 
        1199          994         1973          102          925          847 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         224          186          181          205 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                  2 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              2948               5925 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               412                564 
[1] "2.0 - 2948.0 (412.0)" "2.0 - 5925.0 (564.0)"
[1] "hr=" "1.1"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED        44        6        12        3
  20P GAIN WILD-TYPE      78        5        30        9
D35V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                 44                 78
  STAGE II                 6                  5
  STAGE III               12                 30
  STAGE IV                 3                  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                 T1 T2 T3+T4
  20P GAIN MUTATED   47  8    14
  20P GAIN WILD-TYPE 83 10    36
D35V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                  47                 83
  T2                   8                 10
  T3+T4               14                 36
[1] 3 2
[1] 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   10  6  1
  20P GAIN WILD-TYPE 23 14  3
D35V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               10                 23
  N1                6                 14
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  20P GAIN MUTATED   29  2 35
  20P GAIN WILD-TYPE 52  6 61
D35V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               29                 52
  M1                2                  6
  MX               35                 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"
D35V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   22 47
  20P GAIN WILD-TYPE 36 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     22   47
  20P GAIN WILD-TYPE   36   93
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               22                 36
  MALE                 47                 93
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0     1
  20P GAIN WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          14    46
  20P GAIN WILD-TYPE                        35    83
D35V10, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                      14                 35
  WHITE                                          46                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    2 55
  20P GAIN WILD-TYPE  7 98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2   55
  20P GAIN WILD-TYPE    7   98
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               55                 98
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20Q GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    60   2
  20Q GAIN WILD-TYPE 106   5
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                62                111 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 2                  5 
$`20Q GAIN MUTATED`
TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 
         554          582           27           49            2          780 
TCGA-A4-8311 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A5XZ TCGA-A4-A5Y1 TCGA-AL-3468 
         729          597          600            2           87         1636 
TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-3925 
         412           67          223          747          108         1029 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-7268 
         930         1049          379           14           35          671 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
           5          167          771           29          364           84 
TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 
        2948         1533          116          353          414         1093 
TCGA-DW-7841 TCGA-DZ-6132 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6789 
         445         2460          578           10            7          208 
TCGA-G7-6795 TCGA-G7-6797 TCGA-GL-7966 TCGA-HE-A5NF TCGA-HE-A5NI TCGA-IA-A40Y 
        1194          765          112         2072          360           62 
TCGA-IZ-8195 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A562 TCGA-MH-A854 
         677          160          885         1043          292           11 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SQ 
         174           57         1079          508          423          494 
TCGA-SX-A7SS TCGA-Y8-A895 
        1247            2 

$`20Q GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8515 
          21          493            3            7          140          709 
TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5Y0 TCGA-A4-A6HP 
          23          436          379          516          118            4 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 
        1778          923          763         1357           26          595 
TCGA-B1-A47M TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3926 TCGA-B3-A6W5 TCGA-B9-4113 
         659          510           14          307           85         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-A44B 
         857          803          627          460         1338           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
         585          207          102           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 
         792          403          233         3760         2839         1864 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1516          799          612          232          214          218 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 
        3950         1142          744          419          114           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
        1240         2429         1856         1670         1040          757 
TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-7501 
          97           36         1575         1479         1059          446 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
         786          279         1967         5925          393          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NL 
          32          178           91          408         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
         511          608          649          146            2            4 
TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A856 TCGA-O9-A75Z 
         161          391          543          438          541          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-SX-A71S 
        3035         2653         2584         2816          391         1199 
TCGA-SX-A71U TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SU TCGA-Y8-A894 
         994         1973          102          925          847          224 
TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         186          181          205 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 2                  2 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              2948               5925 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               413                543 
[1] "2.0 - 2948.0 (413.0)" "2.0 - 5925.0 (543.0)"
[1] "hr=" "1.1"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED        44        7        13        3
  20Q GAIN WILD-TYPE      78        4        29        9
D36V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                 44                 78
  STAGE II                 7                  4
  STAGE III               13                 29
  STAGE IV                 3                  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                 T1 T2 T3+T4
  20Q GAIN MUTATED   47  9    15
  20Q GAIN WILD-TYPE 83  9    35
D36V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                  47                 83
  T2                   9                  9
  T3+T4               15                 35
[1] 3 2
[1] 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   10  7  1
  20Q GAIN WILD-TYPE 23 13  3
D36V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               10                 23
  N1                7                 13
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  20Q GAIN MUTATED   31  2 35
  20Q GAIN WILD-TYPE 50  6 61
D36V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               31                 50
  M1                2                  6
  MX               35                 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"
D36V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   23 48
  20Q GAIN WILD-TYPE 35 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     23   48
  20Q GAIN WILD-TYPE   35   92
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               23                 35
  MALE                 48                 92
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0     1
  20Q GAIN WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                          14    48
  20Q GAIN WILD-TYPE                        35    81
D36V10, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                      14                 35
  WHITE                                          48                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    2 56
  20Q GAIN WILD-TYPE  7 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2   56
  20Q GAIN WILD-TYPE    7   97
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               56                 97
[1] 2 2
[1] FALSE

Clustering(37) Variable = 21Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    10   0
  21Q GAIN WILD-TYPE 156   7
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                163 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 0                  7 
$`21Q GAIN MUTATED`
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-A6HP TCGA-AT-A5NU TCGA-B9-4117 TCGA-B9-A5W9 
         729          709            4           67           14            5 
TCGA-BQ-5892 TCGA-F9-A8NY TCGA-HE-A5NJ TCGA-Q2-A5QZ 
         364           36         1726           57 

$`21Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 
           7           49            2          140          780           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
         118           87         1778         1636          412          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
         763         1357           26          595          223          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
         747          108          510           14         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379           85         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         803          627           35          460         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
          64          585          207          102          167           52 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
        2639          586          270         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 
         792          921          792          771          403          233 
TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
          29           84         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1533         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         218          116          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6789 
         578          757           97           10            7          208 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
        1575         1479         1194         1059          765          446 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         786          279         1967         5925          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
         841           32          178           91         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
         360          167          511          608           62          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
         649          146            2            4          160          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          391          543          438          292 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
          11          541          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          391          174         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         508          423         1973          102          925          494 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
        1247          847          224            2          186          181 
TCGA-Y8-A8RZ 
         205 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                  2 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              1726               5925 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                62                511 
[1] "4.0 - 1726.0 (62.0)"  "2.0 - 5925.0 (511.0)"
[1] "hr="     "2.6e+07"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED         7        0         2        1
  21Q GAIN WILD-TYPE     115       11        40       11
D37V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  7                115
  STAGE II                 0                 11
  STAGE III                2                 40
  STAGE IV                 1                 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                  T1  T2 T3+T4
  21Q GAIN MUTATED     8   1     3
  21Q GAIN WILD-TYPE 122  17    47
D37V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                   8                122
  T2                   1                 17
  T3+T4                3                 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"
                    vv
clus                 N0 N1 N2
  21Q GAIN MUTATED    1  2  0
  21Q GAIN WILD-TYPE 32 18  4
D37V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                1                 32
  N1                2                 18
  N2                0                  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 MX
  21Q GAIN MUTATED    2  1  8
  21Q GAIN WILD-TYPE 79  7 88
D37V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                2                 79
  M1                1                  7
  MX                8                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     4   8
  21Q GAIN WILD-TYPE  54 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4    8
  21Q GAIN WILD-TYPE   54  132
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                4                 54
  MALE                  8                132
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, continuous
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 22 
        TCGA-A4-A48D         TCGA-B1-A654         TCGA-B9-A44B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-A69E         TCGA-G7-A8LD         TCGA-GL-7773 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-HE-A5NI         TCGA-IA-A40U 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-PJ-A5Z9         TCGA-SX-A71S 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-Y8-A894         TCGA-Y8-A896 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ 
"21Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  1     1
  21Q GAIN WILD-TYPE                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           3     6
  21Q GAIN WILD-TYPE                        46   123
D37V10, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                       3                 46
  WHITE                                           6                123
[1] 4 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, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     1  10
  21Q GAIN WILD-TYPE   8 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   10
  21Q GAIN WILD-TYPE    8  143
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               10                143
[1] 2 2
[1] FALSE

Clustering(38) Variable = XQ GAIN MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    57   1
  XQ GAIN WILD-TYPE 109   6
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               58               115 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                 6 
$`XQ GAIN MUTATED`
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A48D 
         729          709           23          597          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU 
         516            2            4         1636          412           67 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         659          747          930           85         1536          857 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W9 
         627           14           35         1338           64            5 
TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-7046 TCGA-BQ-7060 
         167         1454          771           29         2948          214 
TCGA-BQ-7062 TCGA-DW-7836 TCGA-DW-7963 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 
         116         1093         1240            7           36         1575 
TCGA-G7-6795 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI 
        1194          279         5925           91         2072          360 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
        1726          167          160          885          161         1043 
TCGA-MH-A55Z TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-PJ-A5Z9 TCGA-SX-A71U TCGA-SX-A71V 
         391         2653         2584          174          994          508 
TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-Y8-A895 
         102          494         1247            2 

$`XQ GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8518 
           7           49            2          140          780          600 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
         118           87         1778          923          763         1357 
TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
          26          595          223          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-5155 
        1029          307         1049          379          803          460 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 
         671          585          207          102           52         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         586          270         1938         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         792          403          233          364           84         3760 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
         232          218          353          414         3950         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 
         744          419          114          445           92         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        2460         1856         1670         1040          578          757 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 
          97           10          208         1479         1059          765 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
         446          786         1967          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-HE-A5NH TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
          32          178          408          511          608           62 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A560 
         677          649          146            2            4          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
         438          292           11          541          148         3035 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A7SL 
        2816          391           57         1079         1199          423 
TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A898 
        1973          925          847          224          186          181 
TCGA-Y8-A8RZ 
         205 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                 2 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             5925              3950 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              501               510 
[1] "2.0 - 5925.0 (501.0)" "2.0 - 3950.0 (510.0)"
[1] "hr=" "3"  
D38V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED        50        2         6        3
  XQ GAIN WILD-TYPE      72        9        36        9
D38V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                50                72
  STAGE II                2                 9
  STAGE III               6                36
  STAGE IV                3                 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                T1 T2 T3+T4
  XQ GAIN MUTATED   52  6     9
  XQ GAIN WILD-TYPE 78 12    41
D38V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1                 52                78
  T2                  6                12
  T3+T4               9                41
[1] 3 2
[1] 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    8  3  0
  XQ GAIN WILD-TYPE 25 17  4
D38V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0               8                25
  N1               3                17
  N2               0                 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 MX
  XQ GAIN MUTATED   24  2 34
  XQ GAIN WILD-TYPE 57  6 62
D38V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0              24                57
  M1               2                 6
  MX              34                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"
D38V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   14 53
  XQ GAIN WILD-TYPE 44 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     14   53
  XQ GAIN WILD-TYPE   44   87
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              14                44
  MALE                53                87
[1] 2 2
[1] FALSE
D38V8, continuous
D38V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  2     1
  XQ GAIN WILD-TYPE                                0     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                          16    41
  XQ GAIN WILD-TYPE                        33    88
D38V10, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                     16                33
  WHITE                                         41                88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    2 54
  XQ GAIN WILD-TYPE  7 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2   54
  XQ GAIN WILD-TYPE    7   99
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              54                99
[1] 2 2
[1] FALSE

Clustering(39) Variable = 1P LOSS MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    16   2
  1P LOSS WILD-TYPE 150   5
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               18               155 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                 5 
$`1P LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-8098 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-A5W8 
         554            3          140          223          307          207 
TCGA-BQ-5875 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7055 TCGA-F9-A4JJ TCGA-F9-A7Q0 
        2639           84         3760          799           97           10 
TCGA-G7-6789 TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-8500 TCGA-PJ-A5Z8 TCGA-Q2-A5QZ 
         208          765          786          841          391           57 

$`1P LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
          21          493          582           27            7           49 
TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
           2          780          729          709           23          597 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 
         600          436          379          516            2          118 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
          87            4         1778         1636          412          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         763         1357           26           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 
         747          108          510           14         1029          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379           85         1536          857          803 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         627           14           35          460         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
          64          585            5          102          167           52 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
         586          270         1938         1454         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
         921          792          771          403          233           29 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
         364         2948         2839         1864         1533         1516 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         612          232          214          218          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92         1240         2429         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF 
        1856         1670         1040          578          757            7 
TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 
          36         1575         1479         1194         1059          446 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM 
         279         1967         5925          393          112           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
         167          511          608           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         146            2            4          160          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          391          543          438          292           11 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         541          148         3035         2653         2584         2816 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
         174         1079         1199          994          508          423 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU 
        1973          102          925          494         1247          847 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         224            2          186          181          205 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                 2 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             3760              5925 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              265               511 
[1] "3.0 - 3760.0 (265.0)" "2.0 - 5925.0 (511.0)"
[1] "hr=" "3.5"
D39V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED         8        2         7        2
  1P LOSS WILD-TYPE     114        9        35       10
D39V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 8               114
  STAGE II                2                 9
  STAGE III               7                35
  STAGE IV                2                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                 T1  T2 T3+T4
  1P LOSS MUTATED     9   2     9
  1P LOSS WILD-TYPE 121  16    41
D39V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1                  9               121
  T2                  2                16
  T3+T4               9                41
[1] 3 2
[1] 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    2  2  1
  1P LOSS WILD-TYPE 31 18  3
D39V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0               2                31
  N1               2                18
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  1P LOSS MUTATED    9  1  9
  1P LOSS WILD-TYPE 72  7 87
D39V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               9                72
  M1               1                 7
  MX               9                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     9  11
  1P LOSS WILD-TYPE  49 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      9   11
  1P LOSS WILD-TYPE   49  129
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               9                49
  MALE                11               129
[1] 2 2
[1] FALSE
D39V8, continuous
D39V9, continuous
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                23 
       TCGA-A4-A48D        TCGA-B1-A654        TCGA-B9-A44B        TCGA-B9-A69E 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-GL-7773        TCGA-GL-A59T        TCGA-HE-A5NI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-HE-A5NJ        TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9        TCGA-SX-A71S 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SS 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     1
  1P LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           6    11
  1P LOSS WILD-TYPE                        43   118
D39V10, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                      6                43
  WHITE                                         11               118
[1] 4 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, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     1  14
  1P LOSS WILD-TYPE   8 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1   14
  1P LOSS WILD-TYPE    8  139
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              14               139
[1] 2 2
[1] FALSE

Clustering(40) Variable = 1Q LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    12   0
  1Q LOSS WILD-TYPE 154   7
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               12               161 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                0                 7 
$`1Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7583 TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B9-A5W8 
         554            3          223          510          307          207 
TCGA-BQ-5894 TCGA-F9-A7Q0 TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-8500 TCGA-PJ-A5Z8 
          84           10          765          786          841          391 

$`1Q LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
          21          493          582           27            7           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
           2          140          780          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
         118           87            4         1778         1636          412 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 
         659          747          108           14         1029          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379           85         1536          857          803 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         627           14           35          460         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
          64          585            5          102          167           52 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
        2639          586          270         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 
         792          921          792          771          403          233 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
          29          364         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1533         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         218          116          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 
         578          757           97            7           36          208 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A4TM 
        1575         1479         1194         1059          446          279 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R 
        1967         5925          393          112           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         511          608           62          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
           2            4          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 
         148         3035         2653         2584         2816          174 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
          57         1079         1199          994          508          423 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU 
        1973          102          925          494         1247          847 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         224            2          186          181          205 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3                 2 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              841              5925 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              349               511 
[1] "3.0 - 841.0 (349.0)"  "2.0 - 5925.0 (511.0)"
[1] "hr="     "2.7e+07"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED         7        2         2        1
  1Q LOSS WILD-TYPE     115        9        40       11
D40V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 7               115
  STAGE II                2                 9
  STAGE III               2                40
  STAGE IV                1                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                 T1  T2 T3+T4
  1Q LOSS MUTATED     8   2     3
  1Q LOSS WILD-TYPE 122  16    47
D40V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1                  8               122
  T2                  2                16
  T3+T4               3                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"
                   vv
clus                N0 N1 N2
  1Q LOSS MUTATED    2  2  0
  1Q LOSS WILD-TYPE 31 18  4
D40V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0               2                31
  N1               2                18
  N2               0                 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 MX
  1Q LOSS MUTATED    6  1  5
  1Q LOSS WILD-TYPE 75  7 91
D40V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               6                75
  M1               1                 7
  MX               5                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     6   7
  1Q LOSS WILD-TYPE  52 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      6    7
  1Q LOSS WILD-TYPE   52  133
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               6                52
  MALE                 7               133
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     1
  1Q LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           3     8
  1Q LOSS WILD-TYPE                        46   121
D40V10, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                      3                46
  WHITE                                          8               121
[1] 4 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, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1  12
  1Q LOSS WILD-TYPE   8 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   12
  1Q LOSS WILD-TYPE    8  141
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              12               141
[1] 2 2
[1] FALSE

Clustering(41) Variable = 3P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    10   3
  3P LOSS WILD-TYPE 156   4
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               13               160 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3                 4 
$`3P LOSS MUTATED`
TCGA-A4-A5Y1 TCGA-AL-3473 TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5892 
          87          763           64          102          270          364 
TCGA-DZ-6131 TCGA-G7-6789 TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ 
        2429          208          112           62            4           57 
TCGA-Y8-A8RZ 
         205 

$`3P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
         516            2          118            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         412          923         1357           26           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
         460         1338          671          585          207            5 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 
         167           52         2639          586         1938         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
        1242          792          921          792          771          403 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 
         233           29           84         3760         2948         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        1093         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
          92         1240         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
         578          757           97           10            7           36 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
        1575         1479         1194         1059          765          446 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
         786          279         1967         5925          393          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          32          178           91         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 
        1726          167          511          608          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         146            2          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
         174         1079         1199          994          508          423 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU 
        1973          102          925          494         1247          847 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
         224            2          186          181 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4                 2 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             2429              5925 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              112               542 
[1] "4.0 - 2429.0 (112.0)" "2.0 - 5925.0 (542.0)"
[1] "hr=" "13" 
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED         2        1         9        3
  3P LOSS WILD-TYPE     120       10        33        9
D41V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 2               120
  STAGE II                1                10
  STAGE III               9                33
  STAGE IV                3                 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                 T1  T2 T3+T4
  3P LOSS MUTATED     3   2    10
  3P LOSS WILD-TYPE 127  16    40
D41V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1                  3               127
  T2                  2                16
  T3+T4              10                40
[1] 3 2
[1] 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    6  5  1
  3P LOSS WILD-TYPE 27 15  3
D41V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0               6                27
  N1               5                15
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  3P LOSS MUTATED    4  2  7
  3P LOSS WILD-TYPE 77  6 89
D41V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0               4                77
  M1               2                 6
  MX               7                89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     5  10
  3P LOSS WILD-TYPE  53 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5   10
  3P LOSS WILD-TYPE   53  130
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               5                53
  MALE                10               130
[1] 2 2
[1] FALSE
D41V8, continuous
D41V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0     1
  3P LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                           3    10
  3P LOSS WILD-TYPE                        46   119
D41V10, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                      3                46
  WHITE                                         10               119
[1] 4 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, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     0  12
  3P LOSS WILD-TYPE   9 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0   12
  3P LOSS WILD-TYPE    9  141
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              12               141
[1] 2 2
[1] FALSE

Clustering(42) Variable = 3Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     1   2
  3Q LOSS WILD-TYPE 165   5
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3               170 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                 5 
$`3Q LOSS MUTATED`
TCGA-BQ-5877 TCGA-G7-6789 TCGA-GL-7966 
         270          208          112 

$`3Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
         516            2          118           87            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
        1636          412          923          763         1357           26 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
          67          595          223          659          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
         510           14         1029          307          930         1049 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
         379           85         1536          857          803          627 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
          14           35          460         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
         585          207            5          102          167           52 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
        2639          586         1938         1454         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
         921          792          771          403          233           29 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
         364           84         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1533         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         218          116          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
         578          757           97           10            7           36 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
        1575         1479         1194         1059          765          446 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
         786          279         1967         5925          393          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          32          178           91         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        1726          167          511          608           62          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
         649          146            2            4          160          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          391          543          438          292 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
          11          541          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
        2816          391          174           57         1079         1199 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
         994          508          423         1973          102          925 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
         494         1247          847          224            2          186 
TCGA-Y8-A898 TCGA-Y8-A8RZ 
         181          205 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              112                 2 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              270              5925 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            208.0             510.5 
[1] "112.0 - 270.0 (208.0)" "2.0 - 5925.0 (510.5)" 
[1] "hr=" "61" 
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED         0        0         2        2
  3Q LOSS WILD-TYPE     122       11        40       10
D42V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 0               122
  STAGE II                0                11
  STAGE III               2                40
  STAGE IV                2                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                 T1  T2 T3+T4
  3Q LOSS MUTATED     0   0     4
  3Q LOSS WILD-TYPE 130  18    46
D42V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1                  0               130
  T2                  0                18
  T3+T4               4                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"
                   vv
clus                N0 N1 N2
  3Q LOSS MUTATED    1  2  1
  3Q LOSS WILD-TYPE 32 18  3
D42V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0               1                32
  N1               2                18
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  3Q LOSS MUTATED    1  1  2
  3Q LOSS WILD-TYPE 80  7 94
D42V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               1                80
  M1               1                 7
  MX               2                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     2   2
  3Q LOSS WILD-TYPE  56 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    2
  3Q LOSS WILD-TYPE   56  138
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               2                56
  MALE                 2               138
[1] 2 2
[1] FALSE
D42V8, continuous
D42V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     0
  3Q LOSS WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           1     2
  3Q LOSS WILD-TYPE                        48   127
D42V10, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      1                48
  WHITE                                          2               127
[1] 4 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, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0   2
  3Q LOSS WILD-TYPE   9 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    2
  3Q LOSS WILD-TYPE    9  151
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               2               151
[1] 2 2
[1] FALSE

Clustering(43) Variable = 4P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    12   2
  4P LOSS WILD-TYPE 154   5
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               14               159 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                 5 
$`4P LOSS MUTATED`
TCGA-A4-7287 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5894 TCGA-DZ-6131 
          21           26          223          307           84         2429 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7966 TCGA-IA-A40Y 
          97           10          446         1967          112           62 
TCGA-J7-8537 TCGA-Q2-A5QZ 
           4           57 

$`4P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
         412          923          763         1357           67          595 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         659          747          108          510           14         1029 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379           85         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
         671           64          585          207            5          102 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
         167           52         2639          586          270         1938 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
        1454         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 
         403          233           29          364         3760         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
         445           92         1240         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 
        1040          578          757            7           36          208 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 
        1575         1479         1194         1059          765          786 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
         279         5925          393          841           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         511          608          677          649          146            2 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         160          885          161         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
         438          292           11          541          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R 
        2653         2584         2816          391          174         1079 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1199          994          508          423         1973          102 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 
         925          494         1247          847          224            2 
TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         186          181          205 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                4                 2 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             2429              5925 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             90.5             543.0 
[1] "4.0 - 2429.0 (90.5)"  "2.0 - 5925.0 (543.0)"
[1] "hr=" "5.9"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P LOSS MUTATED         3        1        14        1
  4P LOSS WILD-TYPE     119       10        28       11
D43V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 3               119
  STAGE II                1                10
  STAGE III              14                28
  STAGE IV                1                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                 T1  T2 T3+T4
  4P LOSS MUTATED     3   2    14
  4P LOSS WILD-TYPE 127  16    36
D43V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1                  3               127
  T2                  2                16
  T3+T4              14                36
[1] 3 2
[1] 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    2  9  0
  4P LOSS WILD-TYPE 31 11  4
D43V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0               2                31
  N1               9                11
  N2               0                 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 MX
  4P LOSS MUTATED    7  1 11
  4P LOSS WILD-TYPE 74  7 85
D43V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0               7                74
  M1               1                 7
  MX              11                85
[1] 3 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
  4P LOSS MUTATED    14   5
  4P LOSS WILD-TYPE  44 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     14    5
  4P LOSS WILD-TYPE   44  135
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              14                44
  MALE                 5               135
[1] 2 2
[1] FALSE
D43V8, continuous
D43V9, continuous
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                22 
       TCGA-A4-A48D        TCGA-B1-A654        TCGA-B9-A44B        TCGA-B9-A69E 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GL-7773        TCGA-GL-A59T        TCGA-HE-A5NI        TCGA-HE-A5NJ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E7 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-P4-A5EB        TCGA-PJ-A5Z9        TCGA-SX-A71S        TCGA-SX-A71U 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SS        TCGA-Y8-A894 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A8RZ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     2
  4P LOSS WILD-TYPE                                2     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                           4    10
  4P LOSS WILD-TYPE                        45   119
D43V10, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 2
  BLACK OR AFRICAN AMERICAN                      4                45
  WHITE                                         10               119
[1] 4 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, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     1  13
  4P LOSS WILD-TYPE   8 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   13
  4P LOSS WILD-TYPE    8  140
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              13               140
[1] 2 2
[1] FALSE

Clustering(44) Variable = 4Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    13   2
  4Q LOSS WILD-TYPE 153   5
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               15               158 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                 5 
$`4Q LOSS MUTATED`
TCGA-A4-7287 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5876 TCGA-BQ-5894 
          21           26          223          307          586           84 
TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7966 
        2429           97           10          446         1967          112 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ 
          62            4           57 

$`4Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
         412          923          763         1357           67          595 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         659          747          108          510           14         1029 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379           85         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
         671           64          585          207            5          102 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 
         167           52         2639          270         1938         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
        1242          792          921          792          771          403 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 
         233           29          364         3760         2948         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        1093         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
          92         1240         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 
         578          757            7           36          208         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM 
        1479         1194         1059          765          786          279 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
        5925          393          841           32          178           91 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         1726          167          511 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
         608          677          649          146            2          160 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          391          543          438 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         292           11          541          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
        2584         2816          391          174         1079         1199 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
         994          508          423         1973          102          925 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
         494         1247          847          224            2          186 
TCGA-Y8-A898 TCGA-Y8-A8RZ 
         181          205 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                 2 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             2429              5925 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               97               542 
[1] "4.0 - 2429.0 (97.0)"  "2.0 - 5925.0 (542.0)"
[1] "hr=" "5.4"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED         4        1        13        2
  4Q LOSS WILD-TYPE     118       10        29       10
D44V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 4               118
  STAGE II                1                10
  STAGE III              13                29
  STAGE IV                2                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                 T1  T2 T3+T4
  4Q LOSS MUTATED     4   3    13
  4Q LOSS WILD-TYPE 126  15    37
D44V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1                  4               126
  T2                  3                15
  T3+T4              13                37
[1] 3 2
[1] 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    3  8  0
  4Q LOSS WILD-TYPE 30 12  4
D44V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0               3                30
  N1               8                12
  N2               0                 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 MX
  4Q LOSS MUTATED    7  2 11
  4Q LOSS WILD-TYPE 74  6 85
D44V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0               7                74
  M1               2                 6
  MX              11                85
[1] 3 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
  4Q LOSS MUTATED    13   7
  4Q LOSS WILD-TYPE  45 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     13    7
  4Q LOSS WILD-TYPE   45  133
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              13                45
  MALE                 7               133
[1] 2 2
[1] FALSE
D44V8, continuous
D44V9, continuous
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                22 
       TCGA-A4-A48D        TCGA-B1-A654        TCGA-B9-A44B        TCGA-B9-A69E 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GL-7773        TCGA-GL-A59T        TCGA-HE-A5NI        TCGA-HE-A5NJ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E7 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-P4-A5EB        TCGA-PJ-A5Z9        TCGA-SX-A71S        TCGA-SX-A71U 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SS        TCGA-Y8-A894 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A8RZ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0     2
  4Q LOSS WILD-TYPE                                2     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                           4    11
  4Q LOSS WILD-TYPE                        45   118
D44V10, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 2
  BLACK OR AFRICAN AMERICAN                      4                45
  WHITE                                         11               118
[1] 4 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, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     1  14
  4Q LOSS WILD-TYPE   8 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1   14
  4Q LOSS WILD-TYPE    8  139
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              14               139
[1] 2 2
[1] FALSE

Clustering(45) Variable = 5P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     3   1
  5P LOSS WILD-TYPE 163   6
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4               169 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                 6 
$`5P LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-BQ-5894 TCGA-F9-A4JJ 
         554           21           84           97 

$`5P LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
         493            3          582           27            7           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
           2          140          780          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
         118           87            4         1778         1636          412 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
           5          102          167           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         792          771          403          233           29          364 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         419          114          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        2460         1856         1670         1040          578          757 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
          10            7           36          208         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
        1194         1059          765          446          786          279 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        1967         5925          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
         167          511          608           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         146            2            4          160          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          391          543          438          292           11 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         541          148         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
         391          174           57         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         508          423         1973          102          925          494 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
        1247          847          224            2          186          181 
TCGA-Y8-A8RZ 
         205 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               21                 2 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              554              5925 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             90.5             510.0 
[1] "21.0 - 554.0 (90.5)"  "2.0 - 5925.0 (510.0)"
[1] "hr=" "29" 
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         1        0         3        2
  5P LOSS WILD-TYPE     121       11        39       10
D45V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 1               121
  STAGE II                0                11
  STAGE III               3                39
  STAGE IV                2                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                 T1  T2 T3+T4
  5P LOSS MUTATED     1   0     6
  5P LOSS WILD-TYPE 129  18    44
D45V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1                  1               129
  T2                  0                18
  T3+T4               6                44
[1] 3 2
[1] 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    0  3  1
  5P LOSS WILD-TYPE 33 17  3
D45V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0               0                33
  N1               3                17
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  5P LOSS MUTATED    1  1  4
  5P LOSS WILD-TYPE 80  7 92
D45V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               1                80
  M1               1                 7
  MX               4                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     5   2
  5P LOSS WILD-TYPE  53 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5    2
  5P LOSS WILD-TYPE   53  138
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               5                53
  MALE                 2               138
[1] 2 2
[1] FALSE
D45V8, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                50 
       TCGA-A4-7828        TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A4ZT        TCGA-A4-A57E 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963        TCGA-EV-5901 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6796 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-J7-8537        TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-SX-A7SN        TCGA-SX-A7SO        TCGA-SX-A7SP        TCGA-SX-A7SQ 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-SX-A7SU 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
D45V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     0
  5P LOSS WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           1     5
  5P LOSS WILD-TYPE                        48   124
D45V10, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      1                48
  WHITE                                          5               124
[1] 4 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, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     1   4
  5P LOSS WILD-TYPE   8 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1    4
  5P LOSS WILD-TYPE    8  149
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO               4               149
[1] 2 2
[1] FALSE

Clustering(46) Variable = 5Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED     4   1
  5Q LOSS WILD-TYPE 162   6
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                5               168 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                 6 
$`5Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-GL-7966 
         554           21           84           97          112 

$`5Q LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
         493            3          582           27            7           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
           2          140          780          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
         118           87            4         1778         1636          412 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
           5          102          167           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         792          771          403          233           29          364 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         419          114          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        2460         1856         1670         1040          578          757 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
          10            7           36          208         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
        1194         1059          765          446          786          279 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        1967         5925          393          841           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         511          608           62          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
           2            4          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         174           57         1079         1199          994          508 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS 
         423         1973          102          925          494         1247 
TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         847          224            2          186          181          205 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               21                 2 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              554              5925 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             97.0             510.5 
[1] "21.0 - 554.0 (97.0)"  "2.0 - 5925.0 (510.5)"
[1] "hr=" "23" 
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         1        0         4        1
  5Q LOSS WILD-TYPE     121       11        38       11
D46V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 1               121
  STAGE II                0                11
  STAGE III               4                38
  STAGE IV                1                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                 T1  T2 T3+T4
  5Q LOSS MUTATED     1   0     6
  5Q LOSS WILD-TYPE 129  18    44
D46V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1                  1               129
  T2                  0                18
  T3+T4               6                44
[1] 3 2
[1] 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    0  4  0
  5Q LOSS WILD-TYPE 33 16  4
D46V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0               0                33
  N1               4                16
  N2               0                 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 MX
  5Q LOSS MUTATED    1  1  4
  5Q LOSS WILD-TYPE 80  7 92
D46V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               1                80
  M1               1                 7
  MX               4                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     5   2
  5Q LOSS WILD-TYPE  53 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5    2
  5Q LOSS WILD-TYPE   53  138
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               5                53
  MALE                 2               138
[1] 2 2
[1] FALSE
D46V8, continuous
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                51 
       TCGA-A4-7828        TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A4ZT        TCGA-A4-A57E 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963        TCGA-EV-5901 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-A4TM        TCGA-G7-A8LD        TCGA-IA-A40U        TCGA-IA-A40X 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-IA-A40Y        TCGA-J7-8537        TCGA-Q2-A5QZ        TCGA-SX-A71R 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SN        TCGA-SX-A7SO        TCGA-SX-A7SP 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-SX-A7SQ        TCGA-SX-A7SS        TCGA-SX-A7SU 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
D46V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  0     0
  5Q LOSS WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                           1     5
  5Q LOSS WILD-TYPE                        48   124
D46V10, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      1                48
  WHITE                                          5               124
[1] 4 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, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     1   4
  5Q LOSS WILD-TYPE   8 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1    4
  5Q LOSS WILD-TYPE    8  149
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO               4               149
[1] 2 2
[1] FALSE

Clustering(47) Variable = 6P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    10   1
  6P LOSS WILD-TYPE 156   6
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               11               162 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                1                 6 
$`6P LOSS MUTATED`
TCGA-A4-7286 TCGA-B3-3926 TCGA-BQ-7056 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 
         554          307          612          578           10          208 
TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-7966 TCGA-SX-A7SL TCGA-Y8-A896 
         765          786          112          423          186 

$`6P LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
          21          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
         412          923          763         1357           26           67 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
         595          223          659          747          108          510 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
          14         1029          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
           5          102          167           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         792          771          403          233           29          364 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
          84         3760         2948         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
        1516          799          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         419          114          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ 
        2460         1856         1670         1040          757           97 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
           7           36         1575         1479         1194         1059 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
         446          279         1967         5925          393          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          32          178           91         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        1726          167          511          608           62          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
         649          146            2            4          160          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          391          543          438          292 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
          11          541          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
        2816          391          174           57         1079         1199 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         994          508         1973          102          925          494 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
        1247          847          224            2          181          205 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               10                 2 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              786              5925 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              423               509 
[1] "10.0 - 786.0 (423.0)" "2.0 - 5925.0 (509.0)"
[1] "hr=" "4.6"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED         5        0         7        2
  6P LOSS WILD-TYPE     117       11        35       10
D47V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 5               117
  STAGE II                0                11
  STAGE III               7                35
  STAGE IV                2                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                 T1  T2 T3+T4
  6P LOSS MUTATED     6   1     8
  6P LOSS WILD-TYPE 124  17    42
D47V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1                  6               124
  T2                  1                17
  T3+T4               8                42
[1] 3 2
[1] 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    2  2  2
  6P LOSS WILD-TYPE 31 18  2
D47V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0               2                31
  N1               2                18
  N2               2                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  6P LOSS MUTATED    8  0  6
  6P LOSS WILD-TYPE 73  8 90
D47V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               8                73
  M1               0                 8
  MX               6                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     7   8
  6P LOSS WILD-TYPE  51 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      7    8
  6P LOSS WILD-TYPE   51  132
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               7                51
  MALE                 8               132
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, continuous
[1] "Remove cluster labels:" "6P LOSS MUTATED"       
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2                22 
       TCGA-A4-A48D        TCGA-B1-A654        TCGA-B9-A44B        TCGA-B9-A69E 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-GL-7773        TCGA-GL-A59T        TCGA-HE-A5NI 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-HE-A5NJ        TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9        TCGA-Q2-A5QZ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SM        TCGA-SX-A7SS 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-Y8-A894        TCGA-Y8-A8RZ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     1
  6P LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           0    11
  6P LOSS WILD-TYPE                        49   118
D47V10, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                      0                49
  WHITE                                         11               118
[1] 4 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, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     0  11
  6P LOSS WILD-TYPE   9 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   11
  6P LOSS WILD-TYPE    9  142
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              11               142
[1] 2 2
[1] FALSE

Clustering(48) Variable = 6Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    14   1
  6Q LOSS WILD-TYPE 152   6
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               15               158 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                1                 6 
$`6Q LOSS MUTATED`
TCGA-A4-7286 TCGA-B3-3926 TCGA-B9-A44B TCGA-BQ-5875 TCGA-BQ-5888 TCGA-BQ-7056 
         554          307           64         2639          403          612 
TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-7502 TCGA-GL-7966 TCGA-J7-8537 
         578           10          208          786          112            4 
TCGA-P4-A5EB TCGA-SX-A7SL TCGA-Y8-A896 
        2584          423          186 

$`6Q LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
          21          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
         412          923          763         1357           26           67 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
         595          223          659          747          108          510 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
          14         1029          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
         460         1338          671          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
         102          167           52          586          270         1938 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
        1454         1242          792          921          792          771 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         233           29          364           84         3760         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 
        2839         1864         1533         1516          799          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        1093         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
          92         1240         2429         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 
        1040          757           97            7           36         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
        1479         1194         1059          765          446          279 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        1967         5925          393          841           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         511          608           62          677          649          146 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
           2          160          885          161         1043          391 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
         543          438          292           11          541          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        3035         2653         2816          391          174           57 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN 
        1079         1199          994          508         1973          102 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 
         925          494         1247          847          224            2 
TCGA-Y8-A898 TCGA-Y8-A8RZ 
         181          205 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                4                 2 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             2639              5925 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            403.0             510.5 
[1] "4.0 - 2639.0 (403.0)" "2.0 - 5925.0 (510.5)"
[1] "hr=" "1.5"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED         7        0         8        2
  6Q LOSS WILD-TYPE     115       11        34       10
D48V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 7               115
  STAGE II                0                11
  STAGE III               8                34
  STAGE IV                2                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                 T1  T2 T3+T4
  6Q LOSS MUTATED     7   0    11
  6Q LOSS WILD-TYPE 123  18    39
D48V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1                  7               123
  T2                  0                18
  T3+T4              11                39
[1] 3 2
[1] 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    3  2  2
  6Q LOSS WILD-TYPE 30 18  2
D48V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0               3                30
  N1               2                18
  N2               2                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  6Q LOSS MUTATED   10  0  6
  6Q LOSS WILD-TYPE 71  8 90
D48V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              10                71
  M1               0                 8
  MX               6                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    10   8
  6Q LOSS WILD-TYPE  48 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     10    8
  6Q LOSS WILD-TYPE   48  132
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              10                48
  MALE                 8               132
[1] 2 2
[1] FALSE
D48V8, continuous
D48V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0     2
  6Q LOSS WILD-TYPE                                2     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           1    12
  6Q LOSS WILD-TYPE                        48   117
D48V10, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 2
  BLACK OR AFRICAN AMERICAN                      1                48
  WHITE                                         12               117
[1] 4 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, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     0  12
  6Q LOSS WILD-TYPE   9 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0   12
  6Q LOSS WILD-TYPE    9  141
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              12               141
[1] 2 2
[1] FALSE

Clustering(49) Variable = 8P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED     6   2
  8P LOSS WILD-TYPE 160   5
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8               165 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                 5 
$`8P LOSS MUTATED`
TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B3-3926 TCGA-DW-5560 TCGA-F9-A7Q0 TCGA-F9-A8NY 
          87          223          307          353           10           36 
TCGA-G7-A8LD TCGA-SX-A7SO 
        1967          925 

$`8P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
         516            2          118            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
         412          923          763         1357           26           67 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         595          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
        1029          930         1049          379           85         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
         857          803          627           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1338          671           64          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         102          167           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
         771          403          233           29          364           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          232          214          218          116 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92         1240         2429         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
        1856         1670         1040          578          757           97 
TCGA-F9-A7VF TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
           7          208         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
         765          446          786          279         5925          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
         112          841           32          178           91         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         408          360         1726          167          511          608 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
          62          677          649          146            2            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         160          885          161         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
         438          292           11          541          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2653         2584         2816          391          174           57 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1079         1199          994          508          423         1973 
TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 
         102          494         1247          847          224            2 
TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         186          181          205 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10                 2 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             1967              5925 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              265               511 
[1] "10.0 - 1967.0 (265.0)" "2.0 - 5925.0 (511.0)" 
[1] "hr=" "11" 
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED         4        1         2        3
  8P LOSS WILD-TYPE     118       10        40        9
D49V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 4               118
  STAGE II                1                10
  STAGE III               2                40
  STAGE IV                3                 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                 T1  T2 T3+T4
  8P LOSS MUTATED     5   1     4
  8P LOSS WILD-TYPE 125  17    46
D49V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1                  5               125
  T2                  1                17
  T3+T4               4                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"
                   vv
clus                N0 N1 N2
  8P LOSS MUTATED    0  5  0
  8P LOSS WILD-TYPE 33 15  4
D49V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0               0                33
  N1               5                15
  N2               0                 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 MX
  8P LOSS MUTATED    4  3  3
  8P LOSS WILD-TYPE 77  5 93
D49V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0               4                77
  M1               3                 5
  MX               3                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     5   5
  8P LOSS WILD-TYPE  53 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5    5
  8P LOSS WILD-TYPE   53  135
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               5                53
  MALE                 5               135
[1] 2 2
[1] FALSE
D49V8, continuous
D49V9, continuous
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                23 
       TCGA-A4-A48D        TCGA-B1-A654        TCGA-B9-A44B        TCGA-B9-A69E 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GL-7773        TCGA-GL-A59T        TCGA-HE-A5NI        TCGA-HE-A5NJ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E7 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-P4-A5EB        TCGA-PJ-A5Z9        TCGA-Q2-A5QZ        TCGA-SX-A71S 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SS 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  0     2
  8P LOSS WILD-TYPE                                2     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                           1     7
  8P LOSS WILD-TYPE                        48   122
D49V10, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 2
  BLACK OR AFRICAN AMERICAN                      1                48
  WHITE                                          7               122
[1] 4 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, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     0  10
  8P LOSS WILD-TYPE   9 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0   10
  8P LOSS WILD-TYPE    9  143
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              10               143
[1] 2 2
[1] FALSE

Clustering(50) Variable = 8Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     3   1
  8Q LOSS WILD-TYPE 163   6
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               169 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                 6 
$`8Q LOSS MUTATED`
TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B3-3926 TCGA-F9-A7Q0 
          87          223          307           10 

$`8Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
         516            2          118            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
         412          923          763         1357           26           67 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         595          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
        1029          930         1049          379           85         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
         857          803          627           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1338          671           64          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         102          167           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
         771          403          233           29          364           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         419          114          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        2460         1856         1670         1040          578          757 
TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
          97            7           36          208         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
        1194         1059          765          446          786          279 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        1967         5925          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
         167          511          608           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         146            2            4          160          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          391          543          438          292           11 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         541          148         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
         391          174           57         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         508          423         1973          102          925          494 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
        1247          847          224            2          186          181 
TCGA-Y8-A8RZ 
         205 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               10                 2 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
              307              5925 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
              155               511 
[1] "10.0 - 307.0 (155.0)" "2.0 - 5925.0 (511.0)"
[1] "hr=" "22" 
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED         2        1         1        1
  8Q LOSS WILD-TYPE     120       10        41       11
D50V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 2               120
  STAGE II                1                10
  STAGE III               1                41
  STAGE IV                1                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                 T1  T2 T3+T4
  8Q LOSS MUTATED     3   1     1
  8Q LOSS WILD-TYPE 127  17    49
D50V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1                  3               127
  T2                  1                17
  T3+T4               1                49
[1] 3 2
[1] 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    0  2  0
  8Q LOSS WILD-TYPE 33 18  4
D50V5, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                55 
       TCGA-A4-7583        TCGA-A4-7585        TCGA-A4-7915        TCGA-A4-A57E 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-A655        TCGA-B1-A656        TCGA-B9-7268 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5885        TCGA-BQ-5887        TCGA-BQ-5888 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7045        TCGA-BQ-7048        TCGA-BQ-7050 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-7051        TCGA-BQ-7056        TCGA-BQ-7058        TCGA-DW-7963 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-F9-A8NY        TCGA-G7-6789        TCGA-G7-6793 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-7501        TCGA-G7-A8LD        TCGA-GL-6846 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GL-7966        TCGA-GL-A59R        TCGA-IA-A40U        TCGA-IA-A40Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-J7-6720        TCGA-J7-8537        TCGA-KV-A74V        TCGA-P4-A5E6 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-P4-A5E8        TCGA-P4-A5EA        TCGA-SX-A71R        TCGA-SX-A7SM 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SX-A7SP        TCGA-SX-A7SS        TCGA-Y8-A8RZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
                   vv
clus                M0 M1 MX
  8Q LOSS MUTATED    2  1  2
  8Q LOSS WILD-TYPE 79  7 94
D50V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               2                79
  M1               1                 7
  MX               2                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     3   2
  8Q LOSS WILD-TYPE  55 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    2
  8Q LOSS WILD-TYPE   55  138
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               3                55
  MALE                 2               138
[1] 2 2
[1] FALSE
D50V8, continuous
D50V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     1
  8Q LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           1     3
  8Q LOSS WILD-TYPE                        48   126
D50V10, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                      1                48
  WHITE                                          3               126
[1] 4 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, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0   5
  8Q LOSS WILD-TYPE   9 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    5
  8Q LOSS WILD-TYPE    9  148
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               5               148
[1] 2 2
[1] FALSE

Clustering(51) Variable = 9P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    16   3
  9P LOSS WILD-TYPE 150   4
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               19               154 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                3                 4 
$`9P LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B9-4116 
         554           21           87           26          307          627 
TCGA-B9-A69E TCGA-BQ-5888 TCGA-BQ-7048 TCGA-BQ-7056 TCGA-DZ-6131 TCGA-F9-A7Q0 
         102          403         2839          612         2429           10 
TCGA-G7-6789 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A8LD TCGA-IA-A40Y TCGA-J7-8537 
         208         1059          446         1967           62            4 
TCGA-Y8-A896 
         186 

$`9P LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
         493            3          582           27            7           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
           2          140          780          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
         118            4         1778         1636          412          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
         763         1357           67          595          223          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 
         747          108          510           14         1029          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379           85         1536          857          803 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
          14           35          460         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
         585          207            5          167           52         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
         586          270         1938         1454         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         921          792          771          233           29          364 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
          84         3760         2948         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         799          232          214          218          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 
         114          445           92         1240         2460         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF 
        1670         1040          578          757           97            7 
TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 
          36         1575         1479         1194          765          786 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
         279         5925          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         167          511          608          677          649          146 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
           2          160          885          161         1043          391 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
         543          438          292           11          541          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3035         2653         2584         2816          391          174 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
          57         1079         1199          994          508          423 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU 
        1973          102          925          494         1247          847 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         224            2          181          205 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                4                 2 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             2839              5925 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            307.0             513.5 
[1] "4.0 - 2839.0 (307.0)" "2.0 - 5925.0 (513.5)"
[1] "hr=" "5.7"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED         5        0        13        5
  9P LOSS WILD-TYPE     117       11        29        7
D51V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 5               117
  STAGE II                0                11
  STAGE III              13                29
  STAGE IV                5                 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                 T1  T2 T3+T4
  9P LOSS MUTATED     6   2    17
  9P LOSS WILD-TYPE 124  16    33
D51V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1                  6               124
  T2                  2                16
  T3+T4              17                33
[1] 3 2
[1] 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    5  8  2
  9P LOSS WILD-TYPE 28 12  2
D51V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0               5                28
  N1               8                12
  N2               2                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  9P LOSS MUTATED    8  3 11
  9P LOSS WILD-TYPE 73  5 85
D51V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0               8                73
  M1               3                 5
  MX              11                85
[1] 3 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
  9P LOSS MUTATED    14  11
  9P LOSS WILD-TYPE  44 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     14   11
  9P LOSS WILD-TYPE   44  129
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              14                44
  MALE                11               129
[1] 2 2
[1] FALSE
D51V8, continuous
D51V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0     2
  9P LOSS WILD-TYPE                                2     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                           2    20
  9P LOSS WILD-TYPE                        47   109
D51V10, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 2
  BLACK OR AFRICAN AMERICAN                      2                47
  WHITE                                         20               109
[1] 4 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, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     0  21
  9P LOSS WILD-TYPE   9 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      0   21
  9P LOSS WILD-TYPE    9  132
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              21               132
[1] 2 2
[1] FALSE

Clustering(52) Variable = 9Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    18   3
  9Q LOSS WILD-TYPE 148   4
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               21               152 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                3                 4 
$`9Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B3-4104 
         554           21           87           26          307         1049 
TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5888 TCGA-BQ-7048 TCGA-BQ-7055 TCGA-BQ-7056 
          64          102          403         2839          799          612 
TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6796 TCGA-G7-7501 
        2429           97           10          208         1059          446 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-Y8-A896 
          62            4          186 

$`9Q LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
         493            3          582           27            7           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
           2          140          780          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
         118            4         1778         1636          412          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
         763         1357           67          595          223          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 
         747          108          510           14         1029          930 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
         379           85         1536          857          803          627 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 
          14           35          460         1338          671          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
         207            5          167           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
         792          771          233           29          364           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
        3760         2948         1864         1533         1516          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        1093         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
          92         1240         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 
         578          757            7           36         1575         1479 
TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 
        1194          765          786          279         1967         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          178           91 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         1726          167          511 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
         608          677          649          146            2          160 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          391          543          438 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         292           11          541          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        2584         2816          391          174           57         1079 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1199          994          508          423         1973          102 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 
         925          494         1247          847          224            2 
TCGA-Y8-A898 TCGA-Y8-A8RZ 
         181          205 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                4                 2 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             2839              5925 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            208.0             528.5 
[1] "4.0 - 2839.0 (208.0)" "2.0 - 5925.0 (528.5)"
[1] "hr=" "6.4"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED         6        1        14        4
  9Q LOSS WILD-TYPE     116       10        28        8
D52V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 6               116
  STAGE II                1                10
  STAGE III              14                28
  STAGE IV                4                 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                 T1  T2 T3+T4
  9Q LOSS MUTATED     7   1    18
  9Q LOSS WILD-TYPE 123  17    32
D52V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1                  7               123
  T2                  1                17
  T3+T4              18                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                N0 N1 N2
  9Q LOSS MUTATED    4  7  2
  9Q LOSS WILD-TYPE 29 13  2
D52V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0               4                29
  N1               7                13
  N2               2                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  9Q LOSS MUTATED   10  2 11
  9Q LOSS WILD-TYPE 71  6 85
D52V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              10                71
  M1               2                 6
  MX              11                85
[1] 3 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
  9Q LOSS MUTATED    14  12
  9Q LOSS WILD-TYPE  44 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     14   12
  9Q LOSS WILD-TYPE   44  128
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              14                44
  MALE                12               128
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     2
  9Q LOSS WILD-TYPE                                2     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           3    20
  9Q LOSS WILD-TYPE                        46   109
D52V10, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 2
  BLACK OR AFRICAN AMERICAN                      3                46
  WHITE                                         20               109
[1] 4 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, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     0  20
  9Q LOSS WILD-TYPE   9 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      0   20
  9Q LOSS WILD-TYPE    9  133
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              20               133
[1] 2 2
[1] FALSE

Clustering(53) Variable = 10P LOSS MUTATION ANALYSIS
D53V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED     9   2
  10P LOSS WILD-TYPE 157   5
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                11                162 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 2                  5 
$`10P LOSS MUTATED`
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B9-4116 TCGA-B9-A44B TCGA-BQ-5876 TCGA-DZ-6131 
          87           26          627           64          586         2429 
TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-7966 TCGA-Q2-A5QZ 
         208          446          786          112           57 

$`10P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
         516            2          118            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
         412          923          763         1357           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
        1536          857          803           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1338          671          585          207            5          102 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 
         167           52         2639          270         1938         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
        1242          792          921          792          771          403 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         233           29          364           84         3760         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
         445           92         1240         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
        1040          578          757           97           10            7 
TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
          36         1575         1479         1194         1059          765 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
         279         1967         5925          393          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
         167          511          608           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         146            2            4          160          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          391          543          438          292           11 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         541          148         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         391          174         1079         1199          994          508 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS 
         423         1973          102          925          494         1247 
TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         847          224            2          186          181          205 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                26                  2 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              2429               5925 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             208.0              510.5 
[1] "26.0 - 2429.0 (208.0)" "2.0 - 5925.0 (510.5)" 
[1] "hr=" "7"  
D53V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED         2        0         7        2
  10P LOSS WILD-TYPE     120       11        35       10
D53V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  2                120
  STAGE II                 0                 11
  STAGE III                7                 35
  STAGE IV                 2                 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                  T1  T2 T3+T4
  10P LOSS MUTATED     3   1     8
  10P LOSS WILD-TYPE 127  17    42
D53V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                   3                127
  T2                   1                 17
  T3+T4                8                 42
[1] 3 2
[1] 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    1  4  1
  10P LOSS WILD-TYPE 32 16  3
D53V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                1                 32
  N1                4                 16
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  10P LOSS MUTATED    1  1  8
  10P LOSS WILD-TYPE 80  7 88
D53V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0                1                 80
  M1                1                  7
  MX                8                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     6   6
  10P LOSS WILD-TYPE  52 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      6    6
  10P LOSS WILD-TYPE   52  134
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                6                 52
  MALE                  6                134
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, continuous
[1] "Remove cluster labels:" "10P LOSS MUTATED"      
clus
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 2                 22 
        TCGA-A4-A48D         TCGA-B1-A654         TCGA-B9-A69E 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-GL-7773         TCGA-GL-A59T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-IA-A40U 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E7 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-PJ-A5Z9         TCGA-SX-A71S 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-Y8-A894         TCGA-Y8-A896 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ 
"10P LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     0
  10P LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           4     8
  10P LOSS WILD-TYPE                        45   121
D53V10, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       4                 45
  WHITE                                           8                121
[1] 4 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, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     0  10
  10P LOSS WILD-TYPE   9 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      0   10
  10P LOSS WILD-TYPE    9  143
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               10                143
[1] 2 2
[1] FALSE

Clustering(54) Variable = 10Q LOSS MUTATION ANALYSIS
D54V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED     9   2
  10Q LOSS WILD-TYPE 157   5
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                11                162 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                  5 
$`10Q LOSS MUTATED`
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B9-A44B TCGA-BQ-5876 TCGA-DZ-6131 TCGA-G7-6789 
          87           26           64          586         2429          208 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-7966 TCGA-J7-8537 TCGA-Q2-A5QZ 
         446          786          112            4           57 

$`10Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
         516            2          118            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
         412          923          763         1357           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
         460         1338          671          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 
         102          167           52         2639          270         1938 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
        1454         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         403          233           29          364           84         3760 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2948         2839         1864         1533         1516          799 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         612          232          214          218          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 
         114          445           92         1240         2460         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
        1670         1040          578          757           97           10 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
           7           36         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
         765          279         1967         5925          393          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          32          178           91         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        1726          167          511          608           62          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         649          146            2          160          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          391          543          438          292           11 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         541          148         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         391          174         1079         1199          994          508 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS 
         423         1973          102          925          494         1247 
TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         847          224            2          186          181          205 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 4                  2 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              2429               5925 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             112.0              513.5 
[1] "4.0 - 2429.0 (112.0)" "2.0 - 5925.0 (513.5)"
[1] "hr=" "7.7"
D54V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED         2        0         8        2
  10Q LOSS WILD-TYPE     120       11        34       10
D54V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  2                120
  STAGE II                 0                 11
  STAGE III                8                 34
  STAGE IV                 2                 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                  T1  T2 T3+T4
  10Q LOSS MUTATED     3   0     9
  10Q LOSS WILD-TYPE 127  18    41
D54V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                   3                127
  T2                   0                 18
  T3+T4                9                 41
[1] 3 2
[1] 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    1  5  1
  10Q LOSS WILD-TYPE 32 15  3
D54V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                1                 32
  N1                5                 15
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  10Q LOSS MUTATED    2  1  8
  10Q LOSS WILD-TYPE 79  7 88
D54V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                2                 79
  M1                1                  7
  MX                8                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     6   6
  10Q LOSS WILD-TYPE  52 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      6    6
  10Q LOSS WILD-TYPE   52  134
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                6                 52
  MALE                  6                134
[1] 2 2
[1] FALSE
D54V8, continuous
D54V9, continuous
[1] "Remove cluster labels:" "10Q LOSS MUTATED"      
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                 22 
        TCGA-A4-A48D         TCGA-B1-A654         TCGA-B9-A69E 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-GL-7773         TCGA-GL-A59T 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-IA-A40U 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E7 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-PJ-A5Z9         TCGA-SX-A71S 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-Y8-A894         TCGA-Y8-A896 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ 
"10Q LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     1
  10Q LOSS WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                           3     8
  10Q LOSS WILD-TYPE                        46   121
D54V10, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                       3                 46
  WHITE                                           8                121
[1] 4 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, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     0  10
  10Q LOSS WILD-TYPE   9 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      0   10
  10Q LOSS WILD-TYPE    9  143
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               10                143
[1] 2 2
[1] FALSE

Clustering(55) Variable = 11P LOSS MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED     7   3
  11P LOSS WILD-TYPE 159   4
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                10                163 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 3                  4 
$`11P LOSS MUTATED`
TCGA-A4-7287 TCGA-B1-7332 TCGA-B3-4104 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-G7-6789 
          21          223         1049          586          270          208 
TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y TCGA-Y8-A896 
         786         1967           62          186 

$`11P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
         412          923          763         1357           26           67 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         595          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
        1029          307          930          379           85         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
         857          803          627           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1338          671           64          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5881 
         102          167           52         2639         1938         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
        1242          792          921          792          771          403 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         233           29          364           84         3760         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
         445           92         1240         2429         2460         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
        1670         1040          578          757           97           10 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
           7           36         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         765          446          279         5925          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
         841           32          178           91         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 
         360         1726          167          511          608          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
         649          146            2            4          160          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          391          543          438          292 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
          11          541          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
        2816          391          174           57         1079         1199 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
         994          508          423         1973          102          925 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A898 
         494         1247          847          224            2          181 
TCGA-Y8-A8RZ 
         205 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                21                  2 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              1967               5925 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             246.5              510.0 
[1] "21.0 - 1967.0 (246.5)" "2.0 - 5925.0 (510.0)" 
[1] "hr=" "18" 
D55V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         3        2         5        2
  11P LOSS WILD-TYPE     119        9        37       10
D55V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  3                119
  STAGE II                 2                  9
  STAGE III                5                 37
  STAGE IV                 2                 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                  T1  T2 T3+T4
  11P LOSS MUTATED     3   2     7
  11P LOSS WILD-TYPE 127  16    43
D55V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                   3                127
  T2                   2                 16
  T3+T4                7                 43
[1] 3 2
[1] 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    1  3  1
  11P LOSS WILD-TYPE 32 17  3
D55V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                1                 32
  N1                3                 17
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  11P LOSS MUTATED    4  1  7
  11P LOSS WILD-TYPE 77  7 89
D55V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                4                 77
  M1                1                  7
  MX                7                 89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     5   7
  11P LOSS WILD-TYPE  53 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5    7
  11P LOSS WILD-TYPE   53  133
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                5                 53
  MALE                  7                133
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 22 
        TCGA-A4-A48D         TCGA-B1-A654         TCGA-B9-A44B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-A69E         TCGA-GL-7773         TCGA-GL-A59T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-IA-A40U 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E7 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-PJ-A5Z9         TCGA-Q2-A5QZ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SS         TCGA-Y8-A894 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ 
"11P LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     0
  11P LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           2     8
  11P LOSS WILD-TYPE                        47   121
D55V10, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       2                 47
  WHITE                                           8                121
[1] 4 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, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     0   8
  11P LOSS WILD-TYPE   9 145
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0    8
  11P LOSS WILD-TYPE    9  145
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                8                145
[1] 2 2
[1] FALSE

Clustering(56) Variable = 11Q LOSS MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED     9   2
  11Q LOSS WILD-TYPE 157   5
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                11                162 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 2                  5 
$`11Q LOSS MUTATED`
TCGA-B1-7332 TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5890 TCGA-BQ-7044 
         223           64          586          270          233         3760 
TCGA-G7-6789 TCGA-G7-7502 TCGA-IA-A40Y TCGA-J7-8537 TCGA-Y8-A896 
         208          786           62            4          186 

$`11Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
         516            2          118           87            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
        1636          412          923          763         1357           26 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
          67          595          659          747          108          510 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
          14         1029          307          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
          85         1536          857          803          627           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 
          35          460         1338          671          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 
           5          102          167           52         2639         1938 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
        1454         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7046 TCGA-BQ-7048 
         403           29          364           84         2948         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        1093         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
          92         1240         2429         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
        1040          578          757           97           10            7 
TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
          36         1575         1479         1194         1059          765 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         446          279         1967         5925          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
         841           32          178           91         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 
         360         1726          167          511          608          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         649          146            2          160          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          391          543          438          292           11 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         541          148         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
         391          174           57         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         508          423         1973          102          925          494 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
        1247          847          224            2          181          205 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 4                  2 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              3760               5925 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             223.0              513.5 
[1] "4.0 - 3760.0 (223.0)" "2.0 - 5925.0 (513.5)"
[1] "hr=" "6.9"
D56V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         2        1         8        4
  11Q LOSS WILD-TYPE     120       10        34        8
D56V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  2                120
  STAGE II                 1                 10
  STAGE III                8                 34
  STAGE IV                 4                  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                  T1  T2 T3+T4
  11Q LOSS MUTATED     2   1    12
  11Q LOSS WILD-TYPE 128  17    38
D56V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                   2                128
  T2                   1                 17
  T3+T4               12                 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"
                    vv
clus                 N0 N1 N2
  11Q LOSS MUTATED    2  4  2
  11Q LOSS WILD-TYPE 31 16  2
D56V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                2                 31
  N1                4                 16
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  11Q LOSS MUTATED    6  2  6
  11Q LOSS WILD-TYPE 75  6 90
D56V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                6                 75
  M1                2                  6
  MX                6                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     6   9
  11Q LOSS WILD-TYPE  52 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      6    9
  11Q LOSS WILD-TYPE   52  131
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                6                 52
  MALE                  9                131
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 2                 22 
        TCGA-A4-A48D         TCGA-B1-A654         TCGA-B9-A69E 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-GL-7773         TCGA-GL-A59T 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-IA-A40U 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E7 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-PJ-A5Z9         TCGA-Q2-A5QZ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SS         TCGA-Y8-A894 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ 
"11Q LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     1
  11Q LOSS WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           3     9
  11Q LOSS WILD-TYPE                        46   120
D56V10, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                       3                 46
  WHITE                                           9                120
[1] 4 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, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     0  10
  11Q LOSS WILD-TYPE   9 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   10
  11Q LOSS WILD-TYPE    9  143
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               10                143
[1] 2 2
[1] FALSE

Clustering(57) Variable = 13Q LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    13   3
  13Q LOSS WILD-TYPE 153   4
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                16                157 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                  4 
$`13Q LOSS MUTATED`
TCGA-A4-7287 TCGA-A4-7915 TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B3-A6W5 TCGA-BQ-5875 
          21            7           26          307           85         2639 
TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LD 
          84           97           10          208          786         1967 
TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ 
         112           62            4           57 

$`13Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 
         554          493            3          582           27           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
           2          140          780          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
         118           87            4         1778         1636          412 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
         923          763         1357           67          595          223 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         659          747          108          510           14         1029 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
         930         1049          379         1536          857          803 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         627           14           35          460         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
          64          585          207            5          102          167 
TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
          52          586          270         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 
         792          921          792          771          403          233 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
          29          364         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1533         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         218          116          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 
         578          757            7           36         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-GL-6846 
        1194         1059          765          446          279         5925 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
         393          841           32          178           91         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         408          360         1726          167          511          608 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
         677          649          146            2          160          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          391          543          438          292 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
          11          541          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          391          174         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         508          423         1973          102          925          494 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
        1247          847          224            2          186          181 
TCGA-Y8-A8RZ 
         205 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 4                  2 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              2639               5925 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              84.5              543.0 
[1] "4.0 - 2639.0 (84.5)"  "2.0 - 5925.0 (543.0)"
[1] "hr=" "11" 
D57V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED         5        1        11        3
  13Q LOSS WILD-TYPE     117       10        31        9
D57V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  5                117
  STAGE II                 1                 10
  STAGE III               11                 31
  STAGE IV                 3                  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                  T1  T2 T3+T4
  13Q LOSS MUTATED     5   2    13
  13Q LOSS WILD-TYPE 125  16    37
D57V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                   5                125
  T2                   2                 16
  T3+T4               13                 37
[1] 3 2
[1] 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    2  7  2
  13Q LOSS WILD-TYPE 31 13  2
D57V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                2                 31
  N1                7                 13
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  13Q LOSS MUTATED    7  1 12
  13Q LOSS WILD-TYPE 74  7 84
D57V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0                7                 74
  M1                1                  7
  MX               12                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    14   6
  13Q LOSS WILD-TYPE  44 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     14    6
  13Q LOSS WILD-TYPE   44  134
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               14                 44
  MALE                  6                134
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, continuous
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 22 
        TCGA-A4-A48D         TCGA-B1-A654         TCGA-B9-A44B 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-A69E         TCGA-GL-7773         TCGA-GL-A59T 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-IA-A40U 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E7 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-PJ-A5Z9         TCGA-SX-A71S 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-Y8-A894         TCGA-Y8-A896 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ 
"13Q LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  0     2
  13Q LOSS WILD-TYPE                                2     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                           4    12
  13Q LOSS WILD-TYPE                        45   117
D57V10, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  2
  BLACK OR AFRICAN AMERICAN                       4                 45
  WHITE                                          12                117
[1] 4 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, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     1  15
  13Q LOSS WILD-TYPE   8 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   15
  13Q LOSS WILD-TYPE    8  138
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               15                138
[1] 2 2
[1] FALSE

Clustering(58) Variable = 14Q LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    28   4
  14Q LOSS WILD-TYPE 138   3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                32                141 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 4                  3 
$`14Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-8098 TCGA-A4-A5Y1 TCGA-AL-3473 
         554           21            3          140           87          763 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B9-4116 
        1357           26          223          510          307          627 
TCGA-B9-A5W8 TCGA-BQ-5876 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5894 TCGA-DZ-6131 
         207          586          921          403           84         2429 
TCGA-DZ-6132 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6796 TCGA-G7-7501 
        2460           97           10          208         1059          446 
TCGA-G7-7502 TCGA-G7-A8LD TCGA-GL-8500 TCGA-IA-A40U TCGA-IA-A40Y TCGA-MH-A854 
         786         1967          841          511           62           11 
TCGA-PJ-A5Z8 TCGA-Q2-A5QZ 
         391           57 

$`14Q LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
         493          582           27            7           49            2 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
         780          729          709           23          597          600 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
         436          379          516            2          118            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-5398 
        1778         1636          412          923           67          595 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 
         659          747          108           14         1029          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379           85         1536          857          803 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
          14           35          460         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
         585            5          102          167           52         2639 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 
         270         1938         1454         1242          792          792 
TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 
         771          233           29          364         3760         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
         445           92         1240         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 
         578          757            7           36         1575         1479 
TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
        1194          765          279         5925          393          112 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          32          178           91         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
        1726          167          608          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
           2            4          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A856 TCGA-O9-A75Z 
         391          543          438          292          541          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-SX-A71R 
        3035         2653         2584         2816          174         1079 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1199          994          508          423         1973          102 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 
         925          494         1247          847          224            2 
TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         186          181          205 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 3                  2 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              2460               5925 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               397                541 
[1] "3.0 - 2460.0 (397.0)" "2.0 - 5925.0 (541.0)"
[1] "hr=" "7"  
D58V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED        14        3        11        6
  14Q LOSS WILD-TYPE     108        8        31        6
D58V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                 14                108
  STAGE II                 3                  8
  STAGE III               11                 31
  STAGE IV                 6                  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                  T1  T2 T3+T4
  14Q LOSS MUTATED    15   4    17
  14Q LOSS WILD-TYPE 115  14    33
D58V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                  15                115
  T2                   4                 14
  T3+T4               17                 33
[1] 3 2
[1] 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    7  8  3
  14Q LOSS WILD-TYPE 26 12  1
D58V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                7                 26
  N1                8                 12
  N2                3                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  14Q LOSS MUTATED   11  3 20
  14Q LOSS WILD-TYPE 70  5 76
D58V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0               11                 70
  M1                3                  5
  MX               20                 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"
D58V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    18  18
  14Q LOSS WILD-TYPE  40 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     18   18
  14Q LOSS WILD-TYPE   40  122
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               18                 40
  MALE                 18                122
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0     1
  14Q LOSS WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                           9    24
  14Q LOSS WILD-TYPE                        40   105
D58V10, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                       9                 40
  WHITE                                          24                105
[1] 4 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, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     1  30
  14Q LOSS WILD-TYPE   8 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   30
  14Q LOSS WILD-TYPE    8  123
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               30                123
[1] 2 2
[1] FALSE

Clustering(59) Variable = 15Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    13   3
  15Q LOSS WILD-TYPE 153   4
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                16                157 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 3                  4 
$`15Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-A5Y1 TCGA-B1-5398 TCGA-B3-3926 TCGA-B9-A5W8 
         554            3           87          595          307          207 
TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6796 TCGA-G7-7502 
          84           97           10          208         1059          786 
TCGA-GL-6846 TCGA-GL-7966 TCGA-PJ-A5Z8 TCGA-Y8-A896 
        5925          112          391          186 

$`15Q LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
          21          493          582           27            7           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
           2          140          780          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
         118            4         1778         1636          412          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M 
         763         1357           26           67          223          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 
         747          108          510           14         1029          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379           85         1536          857          803 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         627           14           35          460         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
          64          585            5          102          167           52 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
        2639          586          270         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 
         792          921          792          771          403          233 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
          29          364         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1533         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         218          116          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 
         578          757            7           36         1575         1479 
TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-7773 
        1194          765          446          279         1967          393 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
         841           32          178           91         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
         360         1726          167          511          608           62 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
         677          649          146            2            4          160 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          391          543          438 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         292           11          541          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
        2584         2816          174           57         1079         1199 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
         994          508          423         1973          102          925 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A898 
         494         1247          847          224            2          181 
TCGA-Y8-A8RZ 
         205 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 3                  2 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              5925               3950 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             207.5              516.0 
[1] "3.0 - 5925.0 (207.5)" "2.0 - 3950.0 (516.0)"
[1] "hr=" "10" 
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED         6        1         9        4
  15Q LOSS WILD-TYPE     116       10        33        8
D59V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  6                116
  STAGE II                 1                 10
  STAGE III                9                 33
  STAGE IV                 4                  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                  T1  T2 T3+T4
  15Q LOSS MUTATED     7   1    13
  15Q LOSS WILD-TYPE 123  17    37
D59V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                   7                123
  T2                   1                 17
  T3+T4               13                 37
[1] 3 2
[1] 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    3  7  1
  15Q LOSS WILD-TYPE 30 13  3
D59V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                3                 30
  N1                7                 13
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  15Q LOSS MUTATED    9  2  9
  15Q LOSS WILD-TYPE 72  6 87
D59V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0                9                 72
  M1                2                  6
  MX                9                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     9  12
  15Q LOSS WILD-TYPE  49 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      9   12
  15Q LOSS WILD-TYPE   49  128
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                9                 49
  MALE                 12                128
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, continuous
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                 23 
        TCGA-A4-A48D         TCGA-B1-A654         TCGA-B9-A44B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-A69E         TCGA-G7-A8LD         TCGA-GL-7773 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-P4-A5EB         TCGA-PJ-A5Z9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71S         TCGA-SX-A71U 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SS 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A8RZ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0     1
  15Q LOSS WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           3    14
  15Q LOSS WILD-TYPE                        46   115
D59V10, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                       3                 46
  WHITE                                          14                115
[1] 4 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, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     1  16
  15Q LOSS WILD-TYPE   8 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1   16
  15Q LOSS WILD-TYPE    8  137
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               16                137
[1] 2 2
[1] FALSE

Clustering(60) Variable = 16P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     1   0
  16P LOSS WILD-TYPE 165   7
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                172 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 0                  7 
$`16P LOSS MUTATED`
TCGA-A4-7287 
          21 

$`16P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
         412          923          763         1357           26           67 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
         595          223          659          747          108          510 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
          14         1029          307          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
          85         1536          857          803          627           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
          35          460         1338          671           64          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
         207            5          102          167           52         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
         586          270         1938         1454         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
         921          792          771          403          233           29 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
         364           84         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1533         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         218          116          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
         578          757           97           10            7           36 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
         208         1575         1479         1194         1059          765 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 
         446          786          279         1967         5925          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
         112          841           32          178           91         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         408          360         1726          167          511          608 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
          62          677          649          146            2            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         160          885          161         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
         438          292           11          541          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2653         2584         2816          391          174           57 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1079         1199          994          508          423         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 
         102          925          494         1247          847          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
           2          186          181          205 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                21                  2 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                21               5925 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                21                509 
[1] "21.0 - 21.0 (21.0)"   "2.0 - 5925.0 (509.0)"
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         1        0         2        1
  16P LOSS WILD-TYPE     121       11        40       11
D60V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  1                121
  STAGE II                 0                 11
  STAGE III                2                 40
  STAGE IV                 1                 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                  T1  T2 T3+T4
  16P LOSS MUTATED     1   0     3
  16P LOSS WILD-TYPE 129  18    47
D60V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                   1                129
  T2                   0                 18
  T3+T4                3                 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"
                    vv
clus                 N0 N1 N2
  16P LOSS MUTATED    1  0  1
  16P LOSS WILD-TYPE 32 20  3
D60V5, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 55 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y1         TCGA-AL-3466 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-A655         TCGA-B1-A656 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5877         TCGA-BQ-5878 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5885 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7045 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7050         TCGA-BQ-7051 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-DW-7963 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-F9-A8NY         TCGA-G7-6789 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-7501         TCGA-G7-A8LD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7966         TCGA-GL-A59R 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40Y         TCGA-J7-6720 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-J7-8537         TCGA-KV-A74V         TCGA-P4-A5E6 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-P4-A5E8         TCGA-P4-A5EA         TCGA-SX-A71R 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SP         TCGA-SX-A7SS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ 
"16P LOSS WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  16P LOSS MUTATED    2  0  2
  16P LOSS WILD-TYPE 79  8 94
D60V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0                2                 79
  M1                0                  8
  MX                2                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3   1
  16P LOSS WILD-TYPE  55 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    1
  16P LOSS WILD-TYPE   55  139
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                3                 55
  MALE                  1                139
[1] 2 2
[1] FALSE
D60V8, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 51 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8310 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A4ZT         TCGA-A4-A57E 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6796         TCGA-G7-6797 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-G7-A4TM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-IA-A40U         TCGA-IA-A40X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-8537         TCGA-Q2-A5QZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A71S         TCGA-SX-A71U 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A71V         TCGA-SX-A7SL         TCGA-SX-A7SM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SN         TCGA-SX-A7SO         TCGA-SX-A7SP 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SQ         TCGA-SX-A7SS         TCGA-SX-A7SU 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D60V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     0
  16P LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           0     2
  16P LOSS WILD-TYPE                        49   127
D60V10, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                182 
        TCGA-A4-7286         TCGA-A4-7288         TCGA-A4-7583 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7584         TCGA-A4-7585         TCGA-A4-7732 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7828         TCGA-A4-7915 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7996         TCGA-A4-7997         TCGA-A4-8098 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-8311         TCGA-A4-8312 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-8630         TCGA-A4-A48D 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A4ZT         TCGA-A4-A57E         TCGA-A4-A5DU 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A5XZ         TCGA-A4-A5Y0         TCGA-A4-A5Y1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A6HP         TCGA-A4-A772         TCGA-AL-3466 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-A5DJ         TCGA-AT-A5NU         TCGA-B1-5398 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B1-A47M         TCGA-B1-A47N 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-A654         TCGA-B1-A655         TCGA-B1-A656 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B3-4104         TCGA-B3-8121         TCGA-B3-A6W5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-A44B         TCGA-B9-A5W7         TCGA-B9-A5W8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-B9-A69E         TCGA-B9-A8YH 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-A8YI         TCGA-BQ-5875         TCGA-BQ-5876 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5883 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-7044         TCGA-BQ-7045 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6133         TCGA-DZ-6134 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F9-A4JJ         TCGA-F9-A7Q0         TCGA-F9-A7VF 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F9-A8NY         TCGA-G7-6789         TCGA-G7-6790 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6795         TCGA-G7-6796 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LD         TCGA-GL-6846 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-7966         TCGA-GL-8500 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-A4EM         TCGA-GL-A59R         TCGA-GL-A59T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40X         TCGA-IA-A40Y 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IZ-8195         TCGA-IZ-8196         TCGA-IZ-A6M8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IZ-A6M9         TCGA-J7-6720         TCGA-J7-8537 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KV-A6GD         TCGA-KV-A6GE         TCGA-KV-A74V 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MH-A55W         TCGA-MH-A55Z         TCGA-MH-A560 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MH-A561         TCGA-MH-A562         TCGA-MH-A854 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MH-A856         TCGA-O9-A75Z         TCGA-P4-A5E6 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-P4-A5E8         TCGA-P4-A5EA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-P4-A5ED         TCGA-PJ-A5Z8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-Q2-A5QZ         TCGA-SX-A71R 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A71V 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SN         TCGA-SX-A7SO 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SQ         TCGA-SX-A7SS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A895         TCGA-Y8-A896 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Y8-A898         TCGA-Y8-A8RZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D60V11, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     0   2
  16P LOSS WILD-TYPE   9 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    2
  16P LOSS WILD-TYPE    9  151
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                2                151
[1] 2 2
[1] FALSE

Clustering(61) Variable = 16Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED     1   2
  16Q LOSS WILD-TYPE 165   5
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 3                170 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                  5 
$`16Q LOSS MUTATED`
TCGA-A4-7287 TCGA-A4-A5Y1 TCGA-G7-A8LD 
          21           87         1967 

$`16Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
           2          118            4         1778         1636          412 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
           5          102          167           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         792          771          403          233           29          364 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
          84         3760         2948         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1516          799          612          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         116          353          414         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        2429         2460         1856         1670         1040          578 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 
         757           97           10            7           36          208 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
        1575         1479         1194         1059          765          446 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
         786          279         5925          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          32          178           91         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        1726          167          511          608           62          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
         649          146            2            4          160          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          391          543          438          292 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
          11          541          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
        2816          391          174           57         1079         1199 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
         994          508          423         1973          102          925 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
         494         1247          847          224            2          186 
TCGA-Y8-A898 TCGA-Y8-A8RZ 
         181          205 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                21                  2 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              1967               5925 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                87                509 
[1] "21.0 - 1967.0 (87.0)" "2.0 - 5925.0 (509.0)"
[1] "hr=" "27" 
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         1        0         4        1
  16Q LOSS WILD-TYPE     121       11        38       11
D61V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  1                121
  STAGE II                 0                 11
  STAGE III                4                 38
  STAGE IV                 1                 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                  T1  T2 T3+T4
  16Q LOSS MUTATED     2   0     4
  16Q LOSS WILD-TYPE 128  18    46
D61V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                   2                128
  T2                   0                 18
  T3+T4                4                 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"
                    vv
clus                 N0 N1 N2
  16Q LOSS MUTATED    1  2  1
  16Q LOSS WILD-TYPE 32 18  3
D61V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                1                 32
  N1                2                 18
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  16Q LOSS MUTATED    2  0  4
  16Q LOSS WILD-TYPE 79  8 92
D61V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0                2                 79
  M1                0                  8
  MX                4                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     3   3
  16Q LOSS WILD-TYPE  55 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    3
  16Q LOSS WILD-TYPE   55  137
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                3                 55
  MALE                  3                137
[1] 2 2
[1] FALSE
D61V8, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 50 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8310 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A4ZT         TCGA-A4-A57E 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6796         TCGA-G7-6797 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-G7-A4TM 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40X         TCGA-IA-A40Y 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-J7-8537         TCGA-Q2-A5QZ         TCGA-SX-A71R 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A71V 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SN 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SX-A7SO         TCGA-SX-A7SP         TCGA-SX-A7SQ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-SX-A7SU 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D61V9, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 23 
        TCGA-A4-A48D         TCGA-B1-A654         TCGA-B9-A44B 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-A69E         TCGA-GL-7773         TCGA-GL-A59T 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-IA-A40U 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E7 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-PJ-A5Z9         TCGA-Q2-A5QZ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SS         TCGA-Y8-A894 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RZ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     0
  16Q LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           0     4
  16Q LOSS WILD-TYPE                        49   125
D61V10, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                 49
  WHITE                                           4                125
[1] 4 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, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     0   4
  16Q LOSS WILD-TYPE   9 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0    4
  16Q LOSS WILD-TYPE    9  149
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                4                149
[1] 2 2
[1] FALSE

Clustering(62) Variable = 17P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED     3   1
  17P LOSS WILD-TYPE 163   6
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 4                169 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 1                  6 
$`17P LOSS MUTATED`
TCGA-A4-7287 TCGA-A4-7915 TCGA-G7-6789 TCGA-Q2-A5QZ 
          21            7          208           57 

$`17P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 
         554          493            3          582           27           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
           2          140          780          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
         118           87            4         1778         1636          412 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
           5          102          167           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         792          771          403          233           29          364 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
          84         3760         2948         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1516          799          612          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         116          353          414         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        2429         2460         1856         1670         1040          578 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 
         757           97           10            7           36         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
        1479         1194         1059          765          446          786 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
         279         1967         5925          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          32          178           91         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        1726          167          511          608           62          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
         649          146            2            4          160          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          391          543          438          292 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
          11          541          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          391          174         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         508          423         1973          102          925          494 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
        1247          847          224            2          186          181 
TCGA-Y8-A8RZ 
         205 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                  2 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               208               5925 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                39                511 
[1] "7.0 - 208.0 (39.0)"   "2.0 - 5925.0 (511.0)"
[1] "hr=" "66" 
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED         1        1         3        4
  17P LOSS WILD-TYPE     121       10        39        8
D62V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  1                121
  STAGE II                 1                 10
  STAGE III                3                 39
  STAGE IV                 4                  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                  T1  T2 T3+T4
  17P LOSS MUTATED     1   2     6
  17P LOSS WILD-TYPE 129  16    44
D62V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                   1                129
  T2                   2                 16
  T3+T4                6                 44
[1] 3 2
[1] 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    2  1  3
  17P LOSS WILD-TYPE 31 19  1
D62V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                2                 31
  N1                1                 19
  N2                3                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  17P LOSS MUTATED    2  2  5
  17P LOSS WILD-TYPE 79  6 91
D62V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0                2                 79
  M1                2                  6
  MX                5                 91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     6   3
  17P LOSS WILD-TYPE  52 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      6    3
  17P LOSS WILD-TYPE   52  137
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                6                 52
  MALE                  3                137
[1] 2 2
[1] FALSE
D62V8, continuous
D62V9, continuous
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 1                 23 
        TCGA-A4-A48D         TCGA-B1-A654         TCGA-B9-A44B 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-A69E         TCGA-G7-A8LD         TCGA-GL-7773 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-P4-A5E7         TCGA-P4-A5EB         TCGA-PJ-A5Z9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SS         TCGA-Y8-A894 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RZ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0     0
  17P LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                           2     6
  17P LOSS WILD-TYPE                        47   123
D62V10, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       2                 47
  WHITE                                           6                123
[1] 4 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, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     0   8
  17P LOSS WILD-TYPE   9 145
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      0    8
  17P LOSS WILD-TYPE    9  145
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                8                145
[1] 2 2
[1] FALSE

Clustering(63) Variable = 18P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    22   4
  18P LOSS WILD-TYPE 144   3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                26                147 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                  3 
$`18P LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-8310 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A656 
         554           21          780           26          223           14 
TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5887 TCGA-BQ-5894 TCGA-BQ-7044 
         307          627          270          771           84         3760 
TCGA-BQ-7048 TCGA-BQ-7059 TCGA-DW-7840 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
        2839          232          114          757           97           10 
TCGA-G7-6789 TCGA-GL-7773 TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ 
         208          393          112           62            4           57 
TCGA-SX-A7SM TCGA-SX-A7SO 
        1973          925 

$`18P LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
         493            3          582           27            7           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
           2          140          729          709           23          597 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 
         600          436          379          516            2          118 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
          87            4         1778         1636          412          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
         763         1357           67          595          659          747 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
         108          510         1029          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
          85         1536          857          803           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
           5          102          167           52         2639          586 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7050 
         403          233           29          364         2948         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7060 TCGA-BQ-7061 
        1533         1516          799          612          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         116          353          414         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         744          419          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7VF 
        2460         1856         1670         1040          578            7 
TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
          36         1575         1479         1194         1059          765 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-8500 
         446          786          279         1967         5925          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          32          178           91         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 
        1726          167          511          608          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         146            2          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
         174         1079         1199          994          508          423 
TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 
         102          494         1247          847          224            2 
TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         186          181          205 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                  2 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              3760               5925 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             227.5              541.0 
[1] "4.0 - 3760.0 (227.5)" "2.0 - 5925.0 (541.0)"
[1] "hr=" "8.1"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED         9        1        15        5
  18P LOSS WILD-TYPE     113       10        27        7
D63V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  9                113
  STAGE II                 1                 10
  STAGE III               15                 27
  STAGE IV                 5                  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                  T1  T2 T3+T4
  18P LOSS MUTATED     9   3    20
  18P LOSS WILD-TYPE 121  15    30
D63V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                   9                121
  T2                   3                 15
  T3+T4               20                 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                 N0 N1 N2
  18P LOSS MUTATED    5  8  2
  18P LOSS WILD-TYPE 28 12  2
D63V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                5                 28
  N1                8                 12
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  18P LOSS MUTATED   14  4 12
  18P LOSS WILD-TYPE 67  4 84
D63V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               14                 67
  M1                4                  4
  MX               12                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    15  17
  18P LOSS WILD-TYPE  43 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     15   17
  18P LOSS WILD-TYPE   43  123
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               15                 43
  MALE                 17                123
[1] 2 2
[1] FALSE
D63V8, continuous
D63V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0     2
  18P LOSS WILD-TYPE                                2     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                           7    20
  18P LOSS WILD-TYPE                        42   109
D63V10, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  2
  BLACK OR AFRICAN AMERICAN                       7                 42
  WHITE                                          20                109
[1] 4 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, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     1  24
  18P LOSS WILD-TYPE   8 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1   24
  18P LOSS WILD-TYPE    8  129
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               24                129
[1] 2 2
[1] FALSE

Clustering(64) Variable = 18Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    21   6
  18Q LOSS WILD-TYPE 145   1
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                27                146 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 6                  1 
$`18Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-8310 TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B1-A656 
         554           21          780           87          223           14 
TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5887 TCGA-BQ-5894 TCGA-BQ-7044 
         307          627          270          771           84         3760 
TCGA-BQ-7048 TCGA-BQ-7059 TCGA-DW-7840 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
        2839          232          114          757           97           10 
TCGA-G7-6789 TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 
         208         1967          393          112           62            4 
TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SO 
          57         1973          925 

$`18Q LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
         493            3          582           27            7           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
           2          140          729          709           23          597 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 
         600          436          379          516            2          118 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
           4         1778         1636          412          923          763 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
        1357           26           67          595          659          747 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
         108          510         1029          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
          85         1536          857          803           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
           5          102          167           52         2639          586 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7050 
         403          233           29          364         2948         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7060 TCGA-BQ-7061 
        1533         1516          799          612          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         116          353          414         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         744          419          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7VF 
        2460         1856         1670         1040          578            7 
TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
          36         1575         1479         1194         1059          765 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM 
         446          786          279         5925          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         167          511          608          677          649          146 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
           2          160          885          161         1043          391 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
         543          438          292           11          541          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3035         2653         2584         2816          391          174 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN 
        1079         1199          994          508          423          102 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
         494         1247          847          224            2          186 
TCGA-Y8-A898 TCGA-Y8-A8RZ 
         181          205 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                  2 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              3760               5925 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             232.0              528.5 
[1] "4.0 - 3760.0 (232.0)" "2.0 - 5925.0 (528.5)"
[1] "hr=" "32" 
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED         9        1        16        5
  18Q LOSS WILD-TYPE     113       10        26        7
D64V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  9                113
  STAGE II                 1                 10
  STAGE III               16                 26
  STAGE IV                 5                  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                  T1  T2 T3+T4
  18Q LOSS MUTATED    10   3    20
  18Q LOSS WILD-TYPE 120  15    30
D64V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                  10                120
  T2                   3                 15
  T3+T4               20                 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                 N0 N1 N2
  18Q LOSS MUTATED    5 10  2
  18Q LOSS WILD-TYPE 28 10  2
D64V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                5                 28
  N1               10                 10
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  18Q LOSS MUTATED   14  4 13
  18Q LOSS WILD-TYPE 67  4 83
D64V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               14                 67
  M1                4                  4
  MX               13                 83
[1] 3 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
  18Q LOSS MUTATED    14  19
  18Q LOSS WILD-TYPE  44 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     14   19
  18Q LOSS WILD-TYPE   44  121
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               14                 44
  MALE                 19                121
[1] 2 2
[1] FALSE
D64V8, continuous
D64V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0     2
  18Q LOSS WILD-TYPE                                2     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                           7    21
  18Q LOSS WILD-TYPE                        42   108
D64V10, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  2
  BLACK OR AFRICAN AMERICAN                       7                 42
  WHITE                                          21                108
[1] 4 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, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     1  25
  18Q LOSS WILD-TYPE   8 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1   25
  18Q LOSS WILD-TYPE    8  128
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               25                128
[1] 2 2
[1] FALSE

Clustering(65) Variable = 19P LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    10   3
  19P LOSS WILD-TYPE 156   4
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                13                160 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                  4 
$`19P LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-8310 TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B9-A44B TCGA-BQ-5876 
         554          780           87          223           64          586 
TCGA-BQ-5891 TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y TCGA-P4-A5EB 
          29          208          786         1967           62         2584 
TCGA-Q2-A5QZ 
          57 

$`19P LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
          21          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
          49            2          140          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
         118            4         1778         1636          412          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         763         1357           26           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
         747          108          510           14         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379           85         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
         671          585          207            5          102          167 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
          52         2639          270         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 
         792          921          792          771          403          233 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
         364           84         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1533         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         218          116          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
         578          757           97           10            7           36 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
        1575         1479         1194         1059          765          446 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
         279         5925          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         167          511          608          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
           2            4          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
         148         3035         2653         2816          391          174 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1079         1199          994          508          423         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 
         102          925          494         1247          847          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
           2          186          181          205 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                29                  2 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              2584               5925 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               223                509 
[1] "29.0 - 2584.0 (223.0)" "2.0 - 5925.0 (509.0)" 
[1] "hr=" "9.6"
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P LOSS MUTATED         3        1         7        1
  19P LOSS WILD-TYPE     119       10        35       11
D65V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  3                119
  STAGE II                 1                 10
  STAGE III                7                 35
  STAGE IV                 1                 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                  T1  T2 T3+T4
  19P LOSS MUTATED     4   1     8
  19P LOSS WILD-TYPE 126  17    42
D65V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                   4                126
  T2                   1                 17
  T3+T4                8                 42
[1] 3 2
[1] 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    1  3  1
  19P LOSS WILD-TYPE 32 17  3
D65V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                1                 32
  N1                3                 17
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  19P LOSS MUTATED    2  0  9
  19P LOSS WILD-TYPE 79  8 87
D65V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0                2                 79
  M1                0                  8
  MX                9                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     5   8
  19P LOSS WILD-TYPE  53 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      5    8
  19P LOSS WILD-TYPE   53  132
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                5                 53
  MALE                  8                132
[1] 2 2
[1] FALSE
D65V8, continuous
D65V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0     0
  19P LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           3    10
  19P LOSS WILD-TYPE                        46   119
D65V10, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       3                 46
  WHITE                                          10                119
[1] 4 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, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0  12
  19P LOSS WILD-TYPE   9 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   12
  19P LOSS WILD-TYPE    9  141
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               12                141
[1] 2 2
[1] FALSE

Clustering(66) Variable = 19Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED     8   4
  19Q LOSS WILD-TYPE 158   3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                161 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                  3 
$`19Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-8310 TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B9-A44B TCGA-BQ-5891 
         554          780           87          223           64           29 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y TCGA-Q2-A5QZ 
          97          208          786         1967           62           57 

$`19Q LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
          21          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
          49            2          140          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
         118            4         1778         1636          412          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         763         1357           26           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
         747          108          510           14         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379           85         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
         671          585          207            5          102          167 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 
          52         2639          586          270         1938         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
        1242          792          921          792          771          403 
TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 
         233          364           84         3760         2948         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        1093         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
          92         1240         2429         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
        1040          578          757           10            7           36 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
        1575         1479         1194         1059          765          446 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
         279         5925          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         167          511          608          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
           2            4          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
         174         1079         1199          994          508          423 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU 
        1973          102          925          494         1247          847 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         224            2          186          181          205 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                29                  2 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              1967               5925 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             152.5              511.0 
[1] "29.0 - 1967.0 (152.5)" "2.0 - 5925.0 (511.0)" 
[1] "hr=" "39" 
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         1        1         8        1
  19Q LOSS WILD-TYPE     121       10        34       11
D66V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  1                121
  STAGE II                 1                 10
  STAGE III                8                 34
  STAGE IV                 1                 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                  T1  T2 T3+T4
  19Q LOSS MUTATED     2   1     9
  19Q LOSS WILD-TYPE 128  17    41
D66V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                   2                128
  T2                   1                 17
  T3+T4                9                 41
[1] 3 2
[1] 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    1  3  1
  19Q LOSS WILD-TYPE 32 17  3
D66V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                1                 32
  N1                3                 17
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  19Q LOSS MUTATED    1  0  9
  19Q LOSS WILD-TYPE 80  8 87
D66V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                1                 80
  M1                0                  8
  MX                9                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     6   6
  19Q LOSS WILD-TYPE  52 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6    6
  19Q LOSS WILD-TYPE   52  134
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                6                 52
  MALE                  6                134
[1] 2 2
[1] FALSE
D66V8, continuous
D66V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     0
  19Q LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           4     8
  19Q LOSS WILD-TYPE                        45   121
D66V10, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       4                 45
  WHITE                                           8                121
[1] 4 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, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     0  11
  19Q LOSS WILD-TYPE   9 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   11
  19Q LOSS WILD-TYPE    9  142
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               11                142
[1] 2 2
[1] FALSE

Clustering(67) Variable = 21Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    26   2
  21Q LOSS WILD-TYPE 140   5
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                28                145 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                  5 
$`21Q LOSS MUTATED`
TCGA-A4-7288 TCGA-A4-8516 TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-AL-3468 TCGA-B3-3925 
         493           23          516            2         1636         1029 
TCGA-B3-3926 TCGA-B9-4114 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-BQ-5875 
         307          857           64          585          207         2639 
TCGA-BQ-5885 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7061 TCGA-DZ-6134 TCGA-F9-A4JJ 
         921          233           84          218         1856           97 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6796 TCGA-GL-7966 TCGA-HE-A5NF TCGA-IA-A40U 
          10          208         1059          112         2072          511 
TCGA-IA-A40Y TCGA-KV-A6GE TCGA-KV-A74V TCGA-PJ-A5Z9 
          62          885          161          174 

$`21Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554           21            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         597          600          436          379          118           87 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
           4         1778          412          923          763         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
          26           67          595          223          659          747 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
         108          510           14          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
          85         1536          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
         460         1338          671            5          102          167 
TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
          52          586          270         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 TCGA-BQ-5892 
         792          792          771          403           29          364 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 
         799          612          232          214          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92         1240         2429         2460 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY 
        1670         1040          578          757            7           36 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
        1575         1479         1194          765          446          786 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
         279         1967         5925          393          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
         178           91          408          360         1726          167 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
         608          677          649          146            2            4 
TCGA-KV-A6GD TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         160         1043          391          543          438          292 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
          11          541          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          391           57         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         508          423         1973          102          925          494 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
        1247          847          224            2          186          181 
TCGA-Y8-A8RZ 
         205 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                  2 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              2639               5925 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               270                541 
[1] "2.0 - 2639.0 (270.0)" "2.0 - 5925.0 (541.0)"
[1] "hr=" "2.3"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED        12        3        11        4
  21Q LOSS WILD-TYPE     110        8        31        8
D67V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                 12                110
  STAGE II                 3                  8
  STAGE III               11                 31
  STAGE IV                 4                  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                  T1  T2 T3+T4
  21Q LOSS MUTATED    13   5    14
  21Q LOSS WILD-TYPE 117  13    36
D67V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                  13                117
  T2                   5                 13
  T3+T4               14                 36
[1] 3 2
[1] 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    5  4  1
  21Q LOSS WILD-TYPE 28 16  3
D67V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                5                 28
  N1                4                 16
  N2                1                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  21Q LOSS MUTATED   11  3 14
  21Q LOSS WILD-TYPE 70  5 82
D67V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               11                 70
  M1                3                  5
  MX               14                 82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    14  18
  21Q LOSS WILD-TYPE  44 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     14   18
  21Q LOSS WILD-TYPE   44  122
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               14                 44
  MALE                 18                122
[1] 2 2
[1] FALSE
D67V8, continuous
D67V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  0     1
  21Q LOSS WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                           5    23
  21Q LOSS WILD-TYPE                        44   106
D67V10, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                       5                 44
  WHITE                                          23                106
[1] 4 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, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     1  25
  21Q LOSS WILD-TYPE   8 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   25
  21Q LOSS WILD-TYPE    8  128
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               25                128
[1] 2 2
[1] FALSE

Clustering(68) Variable = 22Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    38   5
  22Q LOSS WILD-TYPE 128   2
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                43                130 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 5                  2 
$`22Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-8098 TCGA-A4-8517 TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         554          493          140          597          118           87 
TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B9-A44B TCGA-B9-A5W8 
          26          223         1029          307           64          207 
TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5890 TCGA-BQ-5891 
        2639          270          792          921          233           29 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7055 TCGA-BQ-7056 
          84         3760         1864         1533          799          612 
TCGA-BQ-7061 TCGA-DZ-6131 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY 
         218         2429          578           97           10           36 
TCGA-G7-6789 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-7966 TCGA-IA-A40Y 
         208          765          446          786          112           62 
TCGA-J7-8537 TCGA-MH-A856 TCGA-Q2-A5QZ TCGA-SX-A7SL TCGA-SX-A7SM TCGA-Y8-A896 
           4          541           57          423         1973          186 
TCGA-Y8-A8RZ 
         205 

$`22Q LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
          21            3          582           27            7           49 
TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8518 
           2          780          729          709           23          600 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3467 
         436          379          516            2            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        1636          412          923          763         1357           67 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         595          659          747          108          510           14 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379           85         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
         671          585            5          102          167           52 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5886 TCGA-BQ-5887 
         586         1938         1454         1242          792          771 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7059 
         403          364         2948         2839         1516          232 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         214          116          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
        1240         2460         1856         1670         1040          757 
TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-A4TM 
           7         1575         1479         1194         1059          279 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        1967         5925          393          841           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         511          608          677          649          146            2 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         160          885          161         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         438          292           11          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
        2584         2816          391          174         1079         1199 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS 
         994          508          102          925          494         1247 
TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A898 
         847          224            2          181 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 4                  2 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              3760               5925 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             270.0              562.5 
[1] "4.0 - 3760.0 (270.0)" "2.0 - 5925.0 (562.5)"
[1] "hr=" "8.2"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED        14        3        21        7
  22Q LOSS WILD-TYPE     108        8        21        5
D68V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                 14                108
  STAGE II                 3                  8
  STAGE III               21                 21
  STAGE IV                 7                  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                  T1  T2 T3+T4
  22Q LOSS MUTATED    17   3    27
  22Q LOSS WILD-TYPE 113  15    23
D68V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                  17                113
  T2                   3                 15
  T3+T4               27                 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                 N0 N1 N2
  22Q LOSS MUTATED    8 12  2
  22Q LOSS WILD-TYPE 25  8  2
D68V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                8                 25
  N1               12                  8
  N2                2                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  22Q LOSS MUTATED   20  5 20
  22Q LOSS WILD-TYPE 61  3 76
D68V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               20                 61
  M1                5                  3
  MX               20                 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"
D68V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    23  24
  22Q LOSS WILD-TYPE  35 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     23   24
  22Q LOSS WILD-TYPE   35  116
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               23                 35
  MALE                 24                116
[1] 2 2
[1] FALSE
D68V8, continuous
D68V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  0     3
  22Q LOSS WILD-TYPE                                2     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                          10    32
  22Q LOSS WILD-TYPE                        39    97
D68V10, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                  1
  BLACK OR AFRICAN AMERICAN                      10                 39
  WHITE                                          32                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V11, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     3  32
  22Q LOSS WILD-TYPE   6 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3   32
  22Q LOSS WILD-TYPE    6  121
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO               32                121
[1] 2 2
[1] FALSE

Clustering(69) Variable = XQ LOSS MUTATION ANALYSIS
D69V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    12   4
  XQ LOSS WILD-TYPE 154   3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               16               157 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                 3 
$`XQ LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-5155 
         554           21           87          223          307          460 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-DW-5561 TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 
         586          270          414         2429           97           10 
TCGA-G7-7501 TCGA-G7-A8LD TCGA-J7-8537 TCGA-Q2-A5QZ 
         446         1967            4           57 

$`XQ LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
         493            3          582           27            7           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
           2          140          780          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
         118            4         1778         1636          412          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         763         1357           26           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 
         747          108          510           14         1029          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379           85         1536          857          803 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
         627           14           35         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
         585          207            5          102          167           52 
TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
        2639         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         792          771          403          233           29          364 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
          84         3760         2948         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1516          799          612          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         116          353         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 
         419          114          445           92         1240         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF 
        1856         1670         1040          578          757            7 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          36          208         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         765          786          279         5925          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
         841           32          178           91         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
         360         1726          167          511          608           62 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
         677          649          146            2          160          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          391          543          438          292 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
          11          541          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          391          174         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         508          423         1973          102          925          494 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
        1247          847          224            2          186          181 
TCGA-Y8-A8RZ 
         205 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                 2 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             2429              5925 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            288.5             541.0 
[1] "4.0 - 2429.0 (288.5)" "2.0 - 5925.0 (541.0)"
[1] "hr=" "14" 
D69V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED         5        1        10        3
  XQ LOSS WILD-TYPE     117       10        32        9
D69V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 5               117
  STAGE II                1                10
  STAGE III              10                32
  STAGE IV                3                 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                 T1  T2 T3+T4
  XQ LOSS MUTATED     6   1    13
  XQ LOSS WILD-TYPE 124  17    37
D69V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1                  6               124
  T2                  1                17
  T3+T4              13                37
[1] 3 2
[1] 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    2  7  1
  XQ LOSS WILD-TYPE 31 13  3
D69V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0               2                31
  N1               7                13
  N2               1                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  XQ LOSS MUTATED    7  2  9
  XQ LOSS WILD-TYPE 74  6 87
D69V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0               7                74
  M1               2                 6
  MX               9                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    10  10
  XQ LOSS WILD-TYPE  48 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     10   10
  XQ LOSS WILD-TYPE   48  130
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              10                48
  MALE                10               130
[1] 2 2
[1] FALSE
D69V8, continuous
D69V9, continuous
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                22 
       TCGA-A4-A48D        TCGA-B1-A654        TCGA-B9-A44B        TCGA-B9-A69E 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GL-7773        TCGA-GL-A59T        TCGA-HE-A5NI        TCGA-HE-A5NJ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E7 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-P4-A5EB        TCGA-PJ-A5Z9        TCGA-SX-A71S        TCGA-SX-A71U 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SS        TCGA-Y8-A894 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A8RZ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0     2
  XQ LOSS WILD-TYPE                                2     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           6    11
  XQ LOSS WILD-TYPE                        43   118
D69V10, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 2
  BLACK OR AFRICAN AMERICAN                      6                43
  WHITE                                         11               118
[1] 4 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, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0  14
  XQ LOSS WILD-TYPE   9 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   14
  XQ LOSS WILD-TYPE    9  139
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              14               139
[1] 2 2
[1] FALSE
