[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/11541540/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/11548606/transformed.cor.cli.txt"

nPatients in clinical file=223, in cluster file=288, common to both=221
[1] "Reduce the number of clustering variables from 80 to 70."
[1]  70 221
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8               213 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8               213 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               15               206 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               15               206 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               38               183 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               38               183 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               41               180 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               41               180 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               62               159 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               62               159 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               73               148 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               73               148 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               212 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               212 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               213 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               213 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               29               192 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               29               192 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               29               192 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               29               192 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                8               213 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                8               213 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6               215 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6               215 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              130                91 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              130                91 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              131                90 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              131                90 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               14               207 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               14               207 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               18               203 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               18               203 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               218 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               218 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                213 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                213 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                213 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                213 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                10                211 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                10                211 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                10                211 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                10                211 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                91                130 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                91                130 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                91                130 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                91                130 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                23                198 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                23                198 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                218 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                218 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                216 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                216 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               117                104 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               117                104 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               113                108 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               113                108 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               135                 86 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               135                 86 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               149                 72 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               149                 72 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                11                210 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                11                210 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                213 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                213 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                217 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                217 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                217 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                217 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                74                147 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                74                147 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                76                145 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                76                145 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                15                206 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                15                206 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                218 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                218 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               70               151 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               70               151 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               21               200 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               21               200 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               16               205 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               16               205 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               17               204 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               17               204 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                5               216 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                5               216 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               20               201 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               20               201 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               21               200 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               21               200 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                8               213 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                8               213 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                8               213 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                8               213 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               16               205 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               16               205 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               19               202 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               19               202 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               11               210 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               11               210 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                6               215 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                6               215 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               26               195 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               26               195 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               27               194 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               27               194 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                13                208 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                13                208 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                13                208 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                13                208 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                14                207 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                14                207 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                16                205 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                16                205 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                21                200 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                21                200 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                39                182 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                39                182 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                24                197 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                24                197 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                217 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                217 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 6                215 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 6                215 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                214 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                214 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                33                188 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                33                188 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                36                185 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                36                185 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                13                208 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                13                208 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                209 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                209 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                33                188 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                33                188 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                50                171 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                50                171 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               21               200 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               21               200 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [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 221 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 
         207          554           21          493            3           NA 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
          NA          582           27           NA            7           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
           2          140          780          729           NA          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-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
          NA           NA            2          118           87            4 
TCGA-A4-A772 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
          NA           NA         1778         1636          412          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
         763         1357           26           67          595          223 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         659          747          513          108          510           14 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
         200         1029          307          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
         309         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          452          167           52         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
         586          270         1938           NA           NA         1454 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
          NA         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
         403           NA          233           29          364           NA 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
          84         3760           NA         2948         2839           NA 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
        1864         1533         1516          799          612           NA 
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-6133 
         445           92         1240         2429         2460           NA 
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-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
          10            7           36           13          208         1575 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
        1479           NA         1194         1059          765          446 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
         786          194          197          262           NA         2091 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7128 TCGA-HE-7129 
         546           27          341          140           NA           NA 
TCGA-HE-7130 TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
          NA         2072          408          360         1726         2228 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
         167          511          608           62           NA           NA 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 
          NA          677          649          146          376           NA 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
           4          364          885          161         1043          845 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
         924          841          616           11          369          541 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
         493          148         3035         2653           NA           NA 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        2584         2816          391          540          428         1457 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1443         1005          876          823           NA          578 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
        1175           NA         1266          805         1469         1331 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
         579          882          224            2          186          219 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         181          399          205          106          104 
Variable 1:'AGE':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=177,	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=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=6,	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=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=23,	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=25,	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 221 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=52, 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 
146  22  49   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  146    22    51 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
146  22  49   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  146    22    51 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
39 20  4 
[1] "table(vv)"
vv
N0 N1 N2 
39 20  4 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
39 20  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
39 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=19, 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     4   2
  1P GAIN WILD-TYPE 183   5
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6               188 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                 5 
$`1P GAIN MUTATED`
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-G7-6789 TCGA-GL-7966 TCGA-IA-A40Y TCGA-WN-A9G9 
          87           26          208          112           62          579 

$`1P GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
         379          516         1968            2          118            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
          67          595          223          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         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          452 
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-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-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
          10            7           36           13         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          194 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         197          262         1967         1965         5925          393 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
         841           32          378          546           27          341 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         140         2072          408          360         1726         2228 
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 
         376            4          364          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         541          493          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
        2816          391          540          428         1457         1443 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1005          876          823         1973          578         1175 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-AB4C TCGA-Y8-A894 
        1266          805         1469         1331          882          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
           2          186          219          181          399          205 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         106          104 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               26                 2 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              579              5925 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             99.5             550.0 
[1] "26.0 - 579.0 (99.5)"  "2.0 - 5925.0 (550.0)"
[1] "hr=" "66" 
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P GAIN MUTATED         1        0         5        2
  1P GAIN WILD-TYPE     136       16        38       11
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 1               136
  STAGE II                0                16
  STAGE III               5                38
  STAGE IV                2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  1P GAIN MUTATED     2   0     6
  1P GAIN WILD-TYPE 144  22    45
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1                  2               144
  T2                  0                22
  T3+T4               6                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  1
  1P GAIN WILD-TYPE 39 16  3
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0               0                39
  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
  1P GAIN MUTATED     1   1   6
  1P GAIN WILD-TYPE  87   7 106
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               1                87
  M1               1                 7
  MX               6               106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     5   3
  1P GAIN WILD-TYPE  58 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      5    3
  1P GAIN WILD-TYPE   58  155
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               5                58
  MALE                 3               155
[1] 2 2
[1] FALSE
D1V8, continuous
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                55 
       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-A8LB        TCGA-G7-A8LC 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-IA-A40U        TCGA-IA-A40X 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-J7-8537        TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A7SN        TCGA-SX-A7SO        TCGA-SX-A7SP        TCGA-SX-A7SQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-SX-A7SU 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V9, continuous
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                34 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-B1-A654 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A69E        TCGA-F9-A97G        TCGA-G7-A8LB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A59T 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A83S        TCGA-IZ-A6M8        TCGA-MH-A854 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-Y8-A894 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A8RZ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     0
  1P GAIN WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           0     7
  1P GAIN WILD-TYPE                        52   140
D1V10, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      0                52
  WHITE                                          7               140
[1] 4 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   7
  1P GAIN WILD-TYPE   9 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    7
  1P GAIN WILD-TYPE    9  168
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               7               168
[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 178   4
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               12               182 
  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-WN-A9G9 
          29          208         1967          112           62          579 

$`1Q GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207          554          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
         516         1968            2          118            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-A47O TCGA-B1-A654 
         595          223          659          747          513          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         510           14          200         1029          307          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379          309         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          452          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-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-5894 
        1242          792          792          403          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-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
          97           10            7           36           13         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-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         194          197          262         1965         5925          393 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
         841           32          378          546           27          341 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         140         2072          408          360         1726         2228 
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 
         376            4          364          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         541          493          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
        2816          391          540          428         1457         1443 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1005          876          823         1973          578         1175 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-AB4C TCGA-Y8-A894 
        1266          805         1469         1331          882          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
           2          186          219          181          399          205 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         106          104 

  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 
              160               550 
[1] "21.0 - 1967.0 (160.0)" "2.0 - 5925.0 (550.0)" 
[1] "hr=" "22" 
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED         2        0        10        3
  1Q GAIN WILD-TYPE     135       16        33       10
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 2               135
  STAGE II                0                16
  STAGE III              10                33
  STAGE IV                3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  1Q GAIN MUTATED     3   0    12
  1Q GAIN WILD-TYPE 143  22    39
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1                  3               143
  T2                  0                22
  T3+T4              12                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
  1Q GAIN MUTATED    4  6  1
  1Q GAIN WILD-TYPE 35 14  3
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0               4                35
  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  83   6 104
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0               5                83
  M1               2                 6
  MX               8               104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     7   8
  1Q GAIN WILD-TYPE  56 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      7    8
  1Q GAIN WILD-TYPE   56  150
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               7                56
  MALE                 8               150
[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                33 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-B1-A654 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A69E        TCGA-F9-A97G        TCGA-G7-A8LB 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A59T        TCGA-GL-A9DD 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK        TCGA-IA-A40U 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-IA-A83S        TCGA-IZ-A6M8        TCGA-MH-A854        TCGA-MH-A856 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9        TCGA-Q2-A5QZ 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-Y8-A894        TCGA-Y8-A896 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-Y8-A8RZ 
"1Q GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  0     0
  1Q GAIN WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                           0    14
  1Q GAIN WILD-TYPE                        52   133
D2V10, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      0                52
  WHITE                                         14               133
[1] 4 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   9 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      0   13
  1Q GAIN WILD-TYPE    9  162
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              13               162
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    32   1
  2P GAIN WILD-TYPE 155   6
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               33               161 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                1                 6 
$`2P GAIN MUTATED`
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 
         516         1968            2          412           67          223 
TCGA-B3-A6W5 TCGA-B9-4117 TCGA-B9-A44B TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7046 
         309           14           64          364           84         2948 
TCGA-DW-5561 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-A8LC 
         414           36          208         1575         1194          262 
TCGA-GL-7966 TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-IA-A40U TCGA-IA-A40Y 
         112          546         2072          360          511           62 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5EB TCGA-PJ-A5Z9 
         364          885          161         1043         2584          540 
TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SQ 
         428          876         1266 

$`2P GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
         379          118           87            4         1778         1636 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M 
         923          763         1357           26          595          659 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         747          513          108          510           14          200 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        1029          307          930         1049          379         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         857          803          627           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          452          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-5891 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
         233           29         3760         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-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-A97G TCGA-G7-6792 TCGA-G7-6796 
          97           10            7           13         1479         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
         765          446          786          194          197         1967 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        1965         5925          393          841           32          378 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK 
          27          341          140          408         1726         2228 
TCGA-HE-A5NL TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         167          608          677          649          146          376 
TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
           4          845          924          841          616           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL 
        2816          391         1457         1443         1005          823 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
        1973          578         1175          805         1469         1331 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
         579          882          224            2          186          219 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         181          399          205          106          104 

  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 
              412               582 
[1] "2.0 - 2948.0 (412.0)" "2.0 - 5925.0 (582.0)"
[1] "hr=" "1.3"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P GAIN MUTATED        23        2         6        6
  2P GAIN WILD-TYPE     114       14        37        7
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                23               114
  STAGE II                2                14
  STAGE III               6                37
  STAGE IV                6                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  2P GAIN MUTATED    23   5    10
  2P GAIN WILD-TYPE 123  17    41
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1                 23               123
  T2                  5                17
  T3+T4              10                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
  2P GAIN MUTATED    5  7  1
  2P GAIN WILD-TYPE 34 13  3
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0               5                34
  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 20
  2P GAIN WILD-TYPE 78  3 92
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              10                78
  M1               5                 3
  MX              20                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"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    12  26
  2P GAIN WILD-TYPE  51 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     12   26
  2P GAIN WILD-TYPE   51  132
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              12                51
  MALE                26               132
[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     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                           7    27
  2P GAIN WILD-TYPE                        45   120
D3V10, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      7                45
  WHITE                                         27               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"
D3V11, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     2  32
  2P GAIN WILD-TYPE   7 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2   32
  2P GAIN WILD-TYPE    7  143
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              32               143
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    35   1
  2Q GAIN WILD-TYPE 152   6
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               36               158 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                1                 6 
$`2Q GAIN MUTATED`
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-AL-3471 TCGA-AL-7173 TCGA-AT-A5NU 
         516         1968            2          412         1357           67 
TCGA-B1-7332 TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-4117 TCGA-B9-A44B TCGA-BQ-5892 
         223          200          309           14           64          364 
TCGA-BQ-5894 TCGA-BQ-7046 TCGA-DW-5561 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 
          84         2948          414           36          208         1575 
TCGA-G7-6795 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-GL-A59T TCGA-HE-A5NF 
        1194          786          262          112          546         2072 
TCGA-HE-A5NI TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         360          511           62          364          885          161 
TCGA-MH-A55W TCGA-P4-A5EB TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SQ 
        1043         2584          540          428          876         1266 

$`2Q GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
         379          118           87            4         1778         1636 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
         923          763           26          595          659          747 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
         513          108          510           14         1029          307 
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-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 
         627           35          460         1338          671          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
         207            5          452          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-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        3760         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-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-A97G TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
           7           13         1479         1059          765          446 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         194          197         1967         1965         5925          393 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
         841           32          378           27          341          140 
TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X TCGA-IZ-8195 
         408         1726         2228          167          608          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A560 
         649          146          376            4          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
         841          616           11          369          541          493 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-SX-A71R 
         148         3035         2653         2816          391         1457 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1443         1005          823         1973          578         1175 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
         805         1469         1331          579          882          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
           2          186          219          181          399          205 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         106          104 

  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 
            413.0             580.5 
[1] "2.0 - 2948.0 (413.0)" "2.0 - 5925.0 (580.5)"
[1] "hr=" "1.4"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED        25        2         6        7
  2Q GAIN WILD-TYPE     112       14        37        6
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                25               112
  STAGE II                2                14
  STAGE III               6                37
  STAGE IV                7                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  2Q GAIN MUTATED    25   5    11
  2Q GAIN WILD-TYPE 121  17    40
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1                 25               121
  T2                  5                17
  T3+T4              11                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
  2Q GAIN MUTATED    6  7  2
  2Q GAIN WILD-TYPE 33 13  2
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0               6                33
  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   12  5 21
  2Q GAIN WILD-TYPE 76  3 91
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0              12                76
  M1               5                 3
  MX              21                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"
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    13  28
  2Q GAIN WILD-TYPE  50 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     13   28
  2Q GAIN WILD-TYPE   50  130
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              13                50
  MALE                28               130
[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     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                           7    30
  2Q GAIN WILD-TYPE                        45   117
D4V10, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      7                45
  WHITE                                         30               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"
D4V11, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     2  35
  2Q GAIN WILD-TYPE   7 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   35
  2Q GAIN WILD-TYPE    7  140
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              35               140
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    52   0
  3P GAIN WILD-TYPE 135   7
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               52               142 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                0                 7 
$`3P GAIN MUTATED`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-8311 TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-8630 
         207           21          729           23          600          436 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 
         379          516         1636          412           67          223 
TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 
         200          930          309          857           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5886 
         460         1338          671          167         1454          792 
TCGA-BQ-7046 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7836 TCGA-DW-7837 
        2948          214          116          353         1093         1142 
TCGA-DW-7838 TCGA-DW-7963 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-A8LB 
         744         1240           10            7         1575          197 
TCGA-GL-6846 TCGA-GL-A59T TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NL 
        5925          546          341         2072          360          167 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-P4-A5E7 TCGA-PJ-A5Z9 TCGA-SX-A71V 
         364          885          161         2653          540          876 
TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-Y8-A895 
         578         1266         1469            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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
        1968            2          118           87            4         1778 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M 
         923          763         1357           26          595          659 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         747          513          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-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI 
          64          585          207            5          452           52 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5884 
        2639          586          270         1938         1242          792 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         921          771          403          233           29          364 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
          84         3760         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5561 TCGA-DW-7834 
         799          612          232          218          414         3950 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
         419          114          445           92         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-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          36           13          208         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LC TCGA-G7-A8LD 
         765          446          786          194          262         1967 
TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        1965          393          112          841           32          378 
TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A40U 
          27          140          408         1726         2228          511 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         608           62          677          649          146          376 
TCGA-J7-8537 TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
           4         1043          845          924          841          616 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
          11          369          541          493          148         3035 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
        2584         2816          391          428         1457         1443 
TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SR TCGA-SX-A7SU 
        1005          823         1973         1175          805         1331 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
         579          882          224          186          219          181 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         399          205          106          104 

  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 
              488               566 
[1] "2.0 - 5925.0 (488.0)" "2.0 - 3950.0 (566.0)"
[1] "hr="     "2.9e+08"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED        46        5         5        2
  3P GAIN WILD-TYPE      91       11        38       11
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                46                91
  STAGE II                5                11
  STAGE III               5                38
  STAGE IV                2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  3P GAIN MUTATED   47  8     6
  3P GAIN WILD-TYPE 99 14    45
D5V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1                 47                99
  T2                  8                14
  T3+T4               6                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
  3P GAIN MUTATED    7  2  0
  3P GAIN WILD-TYPE 32 18  4
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0               7                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
  3P GAIN MUTATED   26  0 31
  3P GAIN WILD-TYPE 62  8 81
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0              26                62
  M1               0                 8
  MX              31                81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    15  47
  3P GAIN WILD-TYPE  48 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     15   47
  3P GAIN WILD-TYPE   48  111
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              15                48
  MALE                47               111
[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     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                          11    43
  3P GAIN WILD-TYPE                        41   104
D5V10, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                     11                41
  WHITE                                         43               104
[1] 4 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  50
  3P GAIN WILD-TYPE   7 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   50
  3P GAIN WILD-TYPE    7  125
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              50               125
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    61   1
  3Q GAIN WILD-TYPE 126   6
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               62               132 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                 6 
$`3Q GAIN MUTATED`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
         207           21            2          729          709           23 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-AL-3468 
         600          436          379          516            2         1636 
TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-A6W5 
         412           67          223          200          930          309 
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-A8YH TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-7046 
          64          167         1454          792          233         2948 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7963 
         214          116         1093         1142          744         1240 
TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6790 
        2460         1670         1040           10            7         1575 
TCGA-G7-A8LB TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-A59T TCGA-GL-A9DD TCGA-HE-A5NF 
         197         1967         5925          546          341         2072 
TCGA-HE-A5NI TCGA-HE-A5NL TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-P4-A5E6 
         360          167          364          885          161         3035 
TCGA-P4-A5E7 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SQ 
        2653          540          428          876          578         1266 
TCGA-SX-A7SS TCGA-Y8-A895 
        1469            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-A57E TCGA-A4-A5Y0 
          49          140          780          597         1968          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-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
          26          595          659          747          513          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-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1536          803          627          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
         452           52         2639          586          270         1938 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 
        1242          792          921          771          403           29 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
         364           84         3760         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 
        1516          799          612          232          218          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
         414         3950          419          114          445           92 
TCGA-DZ-6131 TCGA-DZ-6134 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY 
        2429         1856          578          757           97           36 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
          13          208         1479         1194         1059          765 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-7773 
         446          786          194          262         1965          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DE 
         112          841           32          378           27          140 
TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
         408         1726         2228          511          608           62 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55W 
         677          649          146          376            4         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         541          493          148         2584         2816          391 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO 
        1457         1443         1005          823         1973         1175 
TCGA-SX-A7SR TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
         805         1331          579          882          224          186 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         219          181          399          205          106          104 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                 3 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             5925              3950 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            528.0             547.5 
[1] "2.0 - 5925.0 (528.0)" "3.0 - 3950.0 (547.5)"
[1] "hr=" "3.2"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED        51        6        10        2
  3Q GAIN WILD-TYPE      86       10        33       11
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                51                86
  STAGE II                6                10
  STAGE III              10                33
  STAGE IV                2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  3Q GAIN MUTATED   53  9    10
  3Q GAIN WILD-TYPE 93 13    41
D6V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1                 53                93
  T2                  9                13
  T3+T4              10                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
  3Q GAIN MUTATED    9  4  0
  3Q GAIN WILD-TYPE 30 16  4
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0               9                30
  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   29  0 38
  3Q GAIN WILD-TYPE 59  8 74
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              29                59
  M1               0                 8
  MX              38                74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    17  56
  3Q GAIN WILD-TYPE  46 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     17   56
  3Q GAIN WILD-TYPE   46  102
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              17                46
  MALE                56               102
[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     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                          14    48
  3Q GAIN WILD-TYPE                        38    99
D6V10, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                     14                38
  WHITE                                         48                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     2  58
  3Q GAIN WILD-TYPE   7 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2   58
  3Q GAIN WILD-TYPE    7  117
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              58               117
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     7   1
  4P GAIN WILD-TYPE 180   6
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8               186 
  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 TCGA-G7-A8LC 
         857            5          364          208         1194          262 
TCGA-SX-A7SR TCGA-WN-AB4C 
         805          882 

$`4P GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         379          516         1968            2          118           87 
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-B1-7332 TCGA-B1-A47M 
        1357           26           67          595          223          659 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         747          513          108          510           14          200 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379          309 
TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
        1536          803          627           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E 
        1338          671           64          585          207          452 
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-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         403          233           29           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-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6796 
           7           36           13         1575         1479         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
         765          446          786          194          197         1967 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        1965         5925          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
         378          546           27          341          140         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
         408          360         1726         2228          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          376 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
           4          364          885          161         1043          845 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
         924          841          616           11          369          541 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         493          148         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
         391          540          428         1457         1443         1005 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         876          823         1973          578         1175         1266 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
        1469         1331          579          224            2          186 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         219          181          399          205          106          104 

  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 
            584.5             540.5 
[1] "5.0 - 1194.0 (584.5)" "2.0 - 5925.0 (540.5)"
[1] "hr=" "7.4"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED         5        1         0        2
  4P GAIN WILD-TYPE     132       15        43       11
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 5               132
  STAGE II                1                15
  STAGE III               0                43
  STAGE IV                2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  4P GAIN MUTATED     5   2     2
  4P GAIN WILD-TYPE 141  20    49
D7V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1                  5               141
  T2                  2                20
  T3+T4               2                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
  4P GAIN MUTATED    2  1  1
  4P GAIN WILD-TYPE 37 19  3
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               2                37
  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     2   1   5
  4P GAIN WILD-TYPE  86   7 107
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               2                86
  M1               1                 7
  MX               5               107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     2   7
  4P GAIN WILD-TYPE  61 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    7
  4P GAIN WILD-TYPE   61  151
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               2                61
  MALE                 7               151
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                34 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-B1-A654 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A69E        TCGA-F9-A97G        TCGA-G7-A8LB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A59T 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A83S        TCGA-IZ-A6M8        TCGA-MH-A854 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SS        TCGA-WN-A9G9        TCGA-Y8-A894 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A8RZ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     0
  4P GAIN WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           1     8
  4P GAIN WILD-TYPE                        51   139
D7V10, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                51
  WHITE                                          8               139
[1] 4 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   9
  4P GAIN WILD-TYPE   9 166
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    9
  4P GAIN WILD-TYPE    9  166
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               9               166
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     7   1
  4Q GAIN WILD-TYPE 180   6
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               186 
  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 TCGA-G7-A8LC 
         857            5          364          208         1194          262 
TCGA-SX-A7SR TCGA-WN-AB4C 
         805          882 

$`4Q GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         379          516         1968            2          118           87 
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-B1-7332 TCGA-B1-A47M 
        1357           26           67          595          223          659 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         747          513          108          510           14          200 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379          309 
TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
        1536          803          627           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E 
        1338          671           64          585          207          452 
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-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         403          233           29           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-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6796 
           7           36           13         1575         1479         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
         765          446          786          194          197         1967 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        1965         5925          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
         378          546           27          341          140         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
         408          360         1726         2228          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          376 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
           4          364          885          161         1043          845 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
         924          841          616           11          369          541 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         493          148         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
         391          540          428         1457         1443         1005 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         876          823         1973          578         1175         1266 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
        1469         1331          579          224            2          186 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         219          181          399          205          106          104 

  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 
            584.5             540.5 
[1] "5.0 - 1194.0 (584.5)" "2.0 - 5925.0 (540.5)"
[1] "hr=" "7.4"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED         5        1         0        1
  4Q GAIN WILD-TYPE     132       15        43       12
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 5               132
  STAGE II                1                15
  STAGE III               0                43
  STAGE IV                1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  4Q GAIN MUTATED     5   2     1
  4Q GAIN WILD-TYPE 141  20    50
D8V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1                  5               141
  T2                  2                20
  T3+T4               1                50
[1] 3 2
[1] TRUE
[1] "dimension 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 37 20  3
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               2                37
  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     2   0   5
  4Q GAIN WILD-TYPE  86   8 107
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               2                86
  M1               0                 8
  MX               5               107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     2   6
  4Q GAIN WILD-TYPE  61 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    6
  4Q GAIN WILD-TYPE   61  152
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               2                61
  MALE                 6               152
[1] 2 2
[1] FALSE
D8V8, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                54 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8310        TCGA-A4-8311 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-8312        TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A4ZT 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-7502        TCGA-G7-A4TM        TCGA-G7-A8LB        TCGA-G7-A8LD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-A8LE        TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-J7-8537        TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-SX-A7SN        TCGA-SX-A7SO        TCGA-SX-A7SP        TCGA-SX-A7SQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-SX-A7SU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V9, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                34 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-B1-A654 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A69E        TCGA-F9-A97G        TCGA-G7-A8LB 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A59T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A83S        TCGA-IZ-A6M8        TCGA-MH-A854 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SS        TCGA-WN-A9G9        TCGA-Y8-A894 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A8RZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     0
  4Q GAIN WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           1     7
  4Q GAIN WILD-TYPE                        51   140
D8V10, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                51
  WHITE                                          7               140
[1] 4 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   8
  4Q GAIN WILD-TYPE   9 167
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    8
  4Q GAIN WILD-TYPE    9  167
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               8               167
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    25   1
  5P GAIN WILD-TYPE 162   6
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               26               168 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                1                 6 
$`5P GAIN MUTATED`
TCGA-2K-A9WE TCGA-A4-8098 TCGA-A4-8516 TCGA-A4-A48D TCGA-A4-A57E TCGA-AL-3473 
         207          140           23          379         1968          763 
TCGA-B1-5398 TCGA-B1-A656 TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5887 TCGA-BQ-5891 
         595           14           14            5          771           29 
TCGA-BQ-5892 TCGA-DW-7838 TCGA-DZ-6131 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 
         364          744         2429          578           10          208 
TCGA-G7-A8LC TCGA-GL-A4EM TCGA-HE-A5NK TCGA-IA-A40Y TCGA-KV-A6GD TCGA-P4-A5EB 
         262           32         2228           62          364         2584 
TCGA-Q2-A5QZ TCGA-SX-A7SQ 
         428         1266 

$`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-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
           7           49            2          780          729          709 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 
         597          600          436          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-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
        1357           26           67          223          659          747 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         513          108          510          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         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          452          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-5888 TCGA-BQ-5890 TCGA-BQ-5894 
         792          921          792          403          233           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-7839 
         353          414         3950         1093         1142          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-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY 
        1670         1040          757           97            7           36 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
          13         1575         1479         1194         1059          765 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
         446          786          194          197         1967         1965 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T 
        5925          393          112          841          378          546 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          27          341          140         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-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         146          376            4          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED 
         541          493          148         3035         2653         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         391          540         1457         1443         1005          876 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SR TCGA-SX-A7SS 
         823         1973          578         1175          805         1469 
TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
        1331          579          882          224            2          186 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         219          181          399          205          106          104 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                5                 2 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             2584              5925 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              364               566 
[1] "5.0 - 2584.0 (364.0)" "2.0 - 5925.0 (566.0)"
[1] "hr=" "1"  
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED        14        2         8        3
  5P GAIN WILD-TYPE     123       14        35       10
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                14               123
  STAGE II                2                14
  STAGE III               8                35
  STAGE IV                3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  5P GAIN MUTATED    15   4    10
  5P GAIN WILD-TYPE 131  18    41
D9V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1                 15               131
  T2                  4                18
  T3+T4              10                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
  5P GAIN MUTATED    8  2  1
  5P GAIN WILD-TYPE 31 18  3
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0               8                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
  5P GAIN MUTATED   13  2 13
  5P GAIN WILD-TYPE 75  6 99
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              13                75
  M1               2                 6
  MX              13                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     7  22
  5P GAIN WILD-TYPE  56 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7   22
  5P GAIN WILD-TYPE   56  136
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               7                56
  MALE                22               136
[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     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                           4    21
  5P GAIN WILD-TYPE                        48   126
D9V10, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      4                48
  WHITE                                         21               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"
D9V11, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     0  23
  5P GAIN WILD-TYPE   9 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      0   23
  5P GAIN WILD-TYPE    9  152
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              23               152
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    25   1
  5Q GAIN WILD-TYPE 162   6
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               26               168 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1                 6 
$`5Q GAIN MUTATED`
TCGA-2K-A9WE TCGA-A4-8098 TCGA-A4-8516 TCGA-A4-A48D TCGA-A4-A57E TCGA-AL-3473 
         207          140           23          379         1968          763 
TCGA-B1-5398 TCGA-B1-A656 TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5887 TCGA-BQ-5891 
         595           14           14            5          771           29 
TCGA-BQ-5892 TCGA-DW-7838 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-A8LC 
         364          744          578           10          208          262 
TCGA-GL-A4EM TCGA-HE-A5NK TCGA-IA-A40Y TCGA-KV-A6GD TCGA-P4-A5E6 TCGA-P4-A5EB 
          32         2228           62          364         3035         2584 
TCGA-Q2-A5QZ TCGA-SX-A7SQ 
         428         1266 

$`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-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
           7           49            2          780          729          709 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 
         597          600          436          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-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
        1357           26           67          223          659          747 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         513          108          510          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         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          452          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-5888 TCGA-BQ-5890 TCGA-BQ-5894 
         792          921          792          403          233           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-7839 
         353          414         3950         1093         1142          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-5903 TCGA-F9-A4JJ TCGA-F9-A7VF 
        1856         1670         1040          757           97            7 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          36           13         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
         765          446          786          194          197         1967 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R 
        1965         5925          393          112          841          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
         546           27          341          140         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-A6GE TCGA-KV-A74V 
         649          146          376            4          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          845          924          841          616           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5ED 
         369          541          493          148         2653         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         391          540         1457         1443         1005          876 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SR TCGA-SX-A7SS 
         823         1973          578         1175          805         1469 
TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
        1331          579          882          224            2          186 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         219          181          399          205          106          104 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5                 2 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             3035              5925 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              364               566 
[1] "5.0 - 3035.0 (364.0)" "2.0 - 5925.0 (566.0)"
[1] "hr=" "1"  
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED        14        2         8        3
  5Q GAIN WILD-TYPE     123       14        35       10
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                14               123
  STAGE II                2                14
  STAGE III               8                35
  STAGE IV                3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  5Q GAIN MUTATED    16   4     9
  5Q GAIN WILD-TYPE 130  18    42
D10V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1                 16               130
  T2                  4                18
  T3+T4               9                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
  5Q GAIN MUTATED    7  3  1
  5Q GAIN WILD-TYPE 32 17  3
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0               7                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
  5Q GAIN MUTATED   13  2 13
  5Q GAIN WILD-TYPE 75  6 99
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0              13                75
  M1               2                 6
  MX              13                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     7  22
  5Q GAIN WILD-TYPE  56 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7   22
  5Q GAIN WILD-TYPE   56  136
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               7                56
  MALE                22               136
[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     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           5    20
  5Q GAIN WILD-TYPE                        47   127
D10V10, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      5                47
  WHITE                                         20               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"
D10V11, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  24
  5Q GAIN WILD-TYPE   9 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   24
  5Q GAIN WILD-TYPE    9  151
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              24               151
[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 182   7
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                5               189 
  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          452         2839          414          428 

$`6P GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         379          516         1968            2          118           87 
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-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
        1357           67          595          223          659          747 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         513          108          510           14          200         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
         307          930         1049          379          309         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-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-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2948         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-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
          36           13          208         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
        1059          765          446          786          194          197 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         262         1967         1965         5925          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
         841           32          378          546           27          341 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         140         2072          408          360         1726         2228 
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          376            4          364          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          845          924          841          616           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
        2584         2816          391          540         1457         1443 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1005          876          823         1973          578         1175 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C 
        1266          805         1469         1331          579          882 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
         224            2          186          219          181          399 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         205          106          104 

  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 
              428               546 
[1] "26.0 - 2839.0 (428.0)" "2.0 - 5925.0 (546.0)" 
[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     136       16        38       11
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 1               136
  STAGE II                0                16
  STAGE III               5                38
  STAGE IV                2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  6P GAIN MUTATED     1   0     7
  6P GAIN WILD-TYPE 145  22    44
D11V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1                  1               145
  T2                  0                22
  T3+T4               7                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
  6P GAIN MUTATED    1  3  0
  6P GAIN WILD-TYPE 38 17  4
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0               1                38
  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  86   6 109
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0               2                86
  M1               2                 6
  MX               3               109
[1] 3 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  60 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3    5
  6P GAIN WILD-TYPE   60  153
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               3                60
  MALE                 5               153
[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                33 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-B1-A654 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-F9-A97G        TCGA-G7-A8LB        TCGA-G7-A8LD 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A59T        TCGA-GL-A9DD 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK        TCGA-IA-A40U 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IA-A83S        TCGA-IZ-A6M8        TCGA-MH-A854        TCGA-MH-A856 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9        TCGA-SX-A71S 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-WN-A9G9        TCGA-Y8-A894        TCGA-Y8-A896 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-Y8-A8RZ 
"6P GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0     0
  6P GAIN WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           2     6
  6P GAIN WILD-TYPE                        50   141
D11V10, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      2                50
  WHITE                                          6               141
[1] 4 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   9 167
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0    8
  6P GAIN WILD-TYPE    9  167
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               8               167
[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 184   7
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3               191 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                0                 7 
$`6Q GAIN MUTATED`
TCGA-AL-A5DJ TCGA-DW-5561 TCGA-Q2-A5QZ 
          26          414          428 

$`6Q GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         379          516         1968            2          118           87 
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-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
        1357           67          595          223          659          747 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         513          108          510           14          200         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
         307          930         1049          379          309         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 
         452          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-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-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
          10            7           36           13          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-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
         194          197          262         1967         1965         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          378          546 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          27          341          140         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
        1726         2228          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          376            4          364 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          845          924          841 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
         616           11          369          541          493          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3035         2653         2584         2816          391          540 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1457         1443         1005          876          823         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
         578         1175         1266          805         1469         1331 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
         579          882          224            2          186          219 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         181          399          205          106          104 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               26                 2 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              428              5925 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              414               546 
[1] "26.0 - 428.0 (414.0)" "2.0 - 5925.0 (546.0)"
[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     136       16        40       11
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 1               136
  STAGE II                0                16
  STAGE III               3                40
  STAGE IV                2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  6Q GAIN MUTATED     1   0     5
  6Q GAIN WILD-TYPE 145  22    46
D12V4, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1                  1               145
  T2                  0                22
  T3+T4               5                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
  6Q GAIN MUTATED    0  3  0
  6Q GAIN WILD-TYPE 39 17  4
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0               0                39
  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  87   6 109
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0               1                87
  M1               2                 6
  MX               3               109
[1] 3 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  60 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3    3
  6Q GAIN WILD-TYPE   60  155
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               3                60
  MALE                 3               155
[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                34 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-B1-A654 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A69E        TCGA-F9-A97G        TCGA-G7-A8LB 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A59T 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A83S        TCGA-IZ-A6M8        TCGA-MH-A854 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-WN-A9G9        TCGA-Y8-A894 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A8RZ 
"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     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           2     4
  6Q GAIN WILD-TYPE                        50   143
D12V10, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      2                50
  WHITE                                          4               143
[1] 4 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   9 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0    6
  6Q GAIN WILD-TYPE    9  169
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               6               169
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   115   3
  7P GAIN WILD-TYPE  72   4
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              118                76 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                3                 4 
$`7P GAIN MUTATED`
TCGA-2K-A9WE TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 
         207          493          582           27           49            2 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 
         780          729          709           23          597          436 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 
         516         1968            2            4         1636          412 
TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N 
         923         1357           26           67          659          747 
TCGA-B1-A654 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 
         108           14          200         1029          930          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
         309         1536          857          803           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-5881 
         460         1338          671          585          167         1454 
TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         792          771           29           84         3760         2948 
TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
        1533          232          214          218          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 
         414         3950         1093         1142          744          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 
         445           92         1240         2460         1856         1040 
TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 
         757           10            7           36          208         1575 
TCGA-G7-6795 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
        1194          786          194          197          262         1965 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DD 
        5925          112          841          378          546          341 
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          376          364          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-PJ-A5Z9 
        1043          845          616          148         2653          540 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM 
         428         1457         1443         1005          876         1973 
TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A895 
         578         1266          805         1469         1331            2 
TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
         186          181          399          106 

$`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-A47O TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 
         223          513          510          307         1049          627 
TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 
          64          207            5          452           52         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 
         586          270         1938         1242          921          792 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 
         403          233          364         2839         1864         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DW-7839 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 
         799          612          419         2429         1670          578 
TCGA-F9-A4JJ TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
          97           13         1479         1059          765          446 
TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NK 
        1967          393           32           27          140         2228 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-J7-8537 TCGA-MH-A560 TCGA-MH-A561 
         511          608          677            4          924          841 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E6 TCGA-P4-A5EB 
          11          369          541          493         3035         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-SX-A7SL TCGA-SX-A7SO TCGA-WN-A9G9 TCGA-WN-AB4C 
        2816          391          823         1175          579          882 
TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
         224          219          205          104 

  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 
              543               527 
[1] "2.0 - 5925.0 (543.0)" "3.0 - 3035.0 (527.0)"
[1] "hr=" "1.8"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED        91        7        15        9
  7P GAIN WILD-TYPE      46        9        28        4
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                91                46
  STAGE II                7                 9
  STAGE III              15                28
  STAGE IV                9                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  7P GAIN MUTATED   94 13    22
  7P GAIN WILD-TYPE 52  9    29
D13V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1                 94                52
  T2                 13                 9
  T3+T4              22                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
  7P GAIN MUTATED   17  7  2
  7P GAIN WILD-TYPE 22 13  2
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              17                22
  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   48  5 68
  7P GAIN WILD-TYPE 40  3 44
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              48                40
  M1               5                 3
  MX              68                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"
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    30 100
  7P GAIN WILD-TYPE  33  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     30  100
  7P GAIN WILD-TYPE   33   58
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              30                33
  MALE               100                58
[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     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                          29    85
  7P GAIN WILD-TYPE                        23    62
D13V10, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          3                 2
  BLACK OR AFRICAN AMERICAN                     29                23
  WHITE                                         85                62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     4 107
  7P GAIN WILD-TYPE   5  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4  107
  7P GAIN WILD-TYPE    5   68
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             107                68
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   116   3
  7Q GAIN WILD-TYPE  71   4
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              119                75 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                3                 4 
$`7Q GAIN MUTATED`
TCGA-2K-A9WE TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 
         207          493          582           27           49            2 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 
         780          729          709           23          597          436 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 
         516         1968            2            4         1636          412 
TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N 
         923         1357           26           67          659          747 
TCGA-B1-A654 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 
         108           14          200         1029          930          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
         309         1536          857          803           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-5881 
         460         1338          671          585          167         1454 
TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         792          771           29          364           84         3760 
TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
        2948         1533          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-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 
         114          445           92         1240         2460         1856 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 
        1040          757           10            7           36          208 
TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
        1575         1194          786          194          197          262 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T 
        1965         5925          112          841          378          546 
TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
         341         2072          408          360         1726          167 
TCGA-IA-A40Y TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
          62          649          146          376          364          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 
         161         1043          845          616          148         2653 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         540          428         1457         1443         1005          876 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
        1973          578         1266          805         1469         1331 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
           2          186          181          399          106 

$`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-A47O TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 
         223          513          510          307         1049          627 
TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 
          64          207            5          452           52         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 
         586          270         1938         1242          921          792 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 
         403          233         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-F9-A97G TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD 
          13         1479         1059          765          446         1967 
TCGA-GL-7773 TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40U 
         393           32           27          140         2228          511 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-J7-8537 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A854 
         608          677            4          924          841           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-P4-A5ED 
         369          541          493         3035         2584         2816 
TCGA-PJ-A5Z8 TCGA-SX-A7SL TCGA-SX-A7SO TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
         391          823         1175          579          882          224 
TCGA-Y8-A897 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
         219          205          104 

  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 
              540               541 
[1] "2.0 - 5925.0 (540.0)" "3.0 - 3035.0 (541.0)"
[1] "hr=" "1.8"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED        92        7        15        9
  7Q GAIN WILD-TYPE      45        9        28        4
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                92                45
  STAGE II                7                 9
  STAGE III              15                28
  STAGE IV                9                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  7Q GAIN MUTATED   95 13    22
  7Q GAIN WILD-TYPE 51  9    29
D14V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1                 95                51
  T2                 13                 9
  T3+T4              22                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
  7Q GAIN MUTATED   18  7  2
  7Q GAIN WILD-TYPE 21 13  2
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              18                21
  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   49  5 68
  7Q GAIN WILD-TYPE 39  3 44
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              49                39
  M1               5                 3
  MX              68                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"
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    30 101
  7Q GAIN WILD-TYPE  33  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     30  101
  7Q GAIN WILD-TYPE   33   57
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              30                33
  MALE               101                57
[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     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                          29    86
  7Q GAIN WILD-TYPE                        23    61
D14V10, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          3                 2
  BLACK OR AFRICAN AMERICAN                     29                23
  WHITE                                         86                61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     4 108
  7Q GAIN WILD-TYPE   5  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4  108
  7Q GAIN WILD-TYPE    5   67
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             108                67
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    11   1
  8P GAIN WILD-TYPE 176   6
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12               182 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                1                 6 
$`8P GAIN MUTATED`
TCGA-A4-8630 TCGA-AL-3471 TCGA-B1-A47O TCGA-B9-A5W9 TCGA-BQ-5887 TCGA-BQ-7056 
         436          412          513            5          771          612 
TCGA-G7-6789 TCGA-GL-7966 TCGA-GL-A4EM TCGA-IZ-8195 TCGA-SX-A71U TCGA-SX-A7SR 
         208          112           32          677         1005          805 

$`8P GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          780 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D 
         729          709           23          597          600          379 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
         516         1968            2          118           87            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
        1778         1636          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-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         510           14          200         1029          307          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379          309         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-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
          64          585          207          452          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-5888 TCGA-BQ-5890 TCGA-BQ-5891 
         792          921          792          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-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1533         1516          799          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-F9-A97G 
         757           97           10            7           36           13 
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-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
         786          194          197          262         1967         1965 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        5925          393          841          378          546           27 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         341          140         2072          408          360         1726 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8196 
        2228          167          511          608           62          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         146          376            4          364          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          845          924          841          616           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        2584         2816          391          540          428         1457 
TCGA-SX-A71S TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1443          876          823         1973          578         1175 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
        1266         1469         1331          579          882          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
           2          186          219          181          399          205 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         106          104 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                5                 2 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             1005              5925 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            474.5             543.5 
[1] "5.0 - 1005.0 (474.5)" "2.0 - 5925.0 (543.5)"
[1] "hr=" "5.1"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         6        2         5        1
  8P GAIN WILD-TYPE     131       14        38       12
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 6               131
  STAGE II                2                14
  STAGE III               5                38
  STAGE IV                1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  8P GAIN MUTATED     6   2     6
  8P GAIN WILD-TYPE 140  20    45
D15V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1                  6               140
  T2                  2                20
  T3+T4               6                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
  8P GAIN MUTATED    3  3  1
  8P GAIN WILD-TYPE 36 17  3
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0               3                36
  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     6   0   8
  8P GAIN WILD-TYPE  82   8 104
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               6                82
  M1               0                 8
  MX               8               104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     6   8
  8P GAIN WILD-TYPE  57 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      6    8
  8P GAIN WILD-TYPE   57  150
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               6                57
  MALE                 8               150
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                33 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-B1-A654 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A69E        TCGA-F9-A97G        TCGA-G7-A8LB 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A59T 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A83S        TCGA-IZ-A6M8        TCGA-MH-A854 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A7SL        TCGA-SX-A7SM 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-WN-A9G9        TCGA-Y8-A894        TCGA-Y8-A896 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-Y8-A8RZ 
"8P GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     0
  8P GAIN WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           0    14
  8P GAIN WILD-TYPE                        52   133
D15V10, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      0                52
  WHITE                                         14               133
[1] 4 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  12
  8P GAIN WILD-TYPE   9 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0   12
  8P GAIN WILD-TYPE    9  163
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              12               163
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    13   1
  8Q GAIN WILD-TYPE 174   6
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               14               180 
  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          428 
TCGA-SX-A71U TCGA-SX-A7SR 
        1005          805 

$`8Q GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          780 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D 
         729          709           23          597          600          379 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
         516         1968            2          118           87            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
        1778         1636          923          763         1357           26 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
          67          595          223          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         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-A69E TCGA-B9-A8YH 
         671           64          585          207          452          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-5888 TCGA-BQ-5890 
        1242          792          921          792          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-7059 TCGA-BQ-7060 
        1864         1533         1516          799          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-A97G 
         578          757           97           10            7           13 
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-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
         786          194          197          262         1967         1965 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        5925          393          841          378          546           27 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         341          140         2072          408          360         1726 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8196 TCGA-IZ-A6M8 
        2228          167          511          608          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         376            4          364          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         541          493          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71V 
        2816          391          540         1457         1443          876 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS 
         823         1973          578         1175         1266         1469 
TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
        1331          579          882          224            2          186 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         219          181          399          205          106          104 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                5                 2 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             1005              5925 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              420               550 
[1] "5.0 - 1005.0 (420.0)" "2.0 - 5925.0 (550.0)"
[1] "hr=" "5.1"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED         5        2         7        4
  8Q GAIN WILD-TYPE     132       14        36        9
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 5               132
  STAGE II                2                14
  STAGE III               7                36
  STAGE IV                4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  8Q GAIN MUTATED     5   2    11
  8Q GAIN WILD-TYPE 141  20    40
D16V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1                  5               141
  T2                  2                20
  T3+T4              11                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
  8Q GAIN MUTATED    2  6  2
  8Q GAIN WILD-TYPE 37 14  2
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0               2                37
  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     6   2  10
  8Q GAIN WILD-TYPE  82   6 102
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0               6                82
  M1               2                 6
  MX              10               102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     9   9
  8Q GAIN WILD-TYPE  54 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      9    9
  8Q GAIN WILD-TYPE   54  149
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               9                54
  MALE                 9               149
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     1
  8Q GAIN WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                           1    16
  8Q GAIN WILD-TYPE                        51   131
D16V10, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      1                51
  WHITE                                         16               131
[1] 4 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  16
  8Q GAIN WILD-TYPE   9 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      0   16
  8Q GAIN WILD-TYPE    9  159
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              16               159
[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 185   7
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2               192 
  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-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         379          516         1968            2          118           87 
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-B1-7332 TCGA-B1-A47M 
        1357           26           67          595          223          659 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         747          513          108          510           14          200 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
        1029          307          930          379          309         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 
         452          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-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
          97           10            7           36           13          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-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
         786          194          197          262         1967         1965 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
        5925          393          841           32          378          546 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          27          341          140         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
        1726         2228          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          376            4          364 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          845          924          841 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
         616           11          369          541          493          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3035         2653         2584         2816          391          540 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
         428         1457         1443         1005          876          823 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
        1973          578         1175         1266          805         1469 
TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
        1331          579          882          224            2          186 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         219          181          399          205          106          104 

  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             540.5 
[1] "112.0 - 1049.0 (580.5)" "2.0 - 5925.0 (540.5)"  
[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     137       15        41       13
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 0               137
  STAGE II                1                15
  STAGE III               2                41
  STAGE IV                0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  9P GAIN MUTATED     0   1     2
  9P GAIN WILD-TYPE 146  21    49
D17V4, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1                  0               146
  T2                  1                21
  T3+T4               2                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
  9P GAIN MUTATED    0  1  1
  9P GAIN WILD-TYPE 39 19  3
D17V5, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                61 
       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-A47O        TCGA-B1-A655 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B1-A656        TCGA-B1-A657        TCGA-B9-7268        TCGA-BQ-5877 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5882 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BQ-5885        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7045        TCGA-BQ-7048        TCGA-BQ-7050 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BQ-7051        TCGA-BQ-7056        TCGA-DW-7963        TCGA-DZ-6131 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-F9-A8NY        TCGA-F9-A97G        TCGA-G7-6789        TCGA-G7-6793 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-7501        TCGA-G7-A8LD        TCGA-GL-6846 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GL-A59R        TCGA-GL-A9DC        TCGA-IA-A40U        TCGA-IA-A40Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IA-A83W        TCGA-J7-6720        TCGA-J7-8537        TCGA-KV-A74V 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-P4-A5E8        TCGA-P4-A5EA        TCGA-SX-A71R 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SP        TCGA-SX-A7SS        TCGA-Y8-A897 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-Y8-A8RZ 
"9P GAIN WILD-TYPE" 
                   vv
clus                 M0  M1  MX
  9P GAIN MUTATED     2   0   1
  9P GAIN WILD-TYPE  86   8 111
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0               2                86
  M1               0                 8
  MX               1               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1   2
  9P GAIN WILD-TYPE  62 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1    2
  9P GAIN WILD-TYPE   62  156
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               1                62
  MALE                 2               156
[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     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           0     3
  9P GAIN WILD-TYPE                        52   144
D17V10, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      0                52
  WHITE                                          3               144
[1] 4 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   9 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0    3
  9P GAIN WILD-TYPE    9  172
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               3               172
[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 181   7
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                188 
  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         1469 

$`10P GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 
          27            7           49            2          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
         516         1968            2          118           87            4 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
        1778          412          923          763         1357           26 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
          67          595          223          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         803          627           14          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          452          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-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-A7VF 
        1670         1040          578          757           97            7 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          13          208         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
         765          446          786          194          197          262 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
        1967         1965         5925          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
          32          378          546           27          341          140 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
        2072          408          360         1726         2228          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 
         376            4          364          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         541          493          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
        2816          391          540          428         1457         1443 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1005          876          823         1973          578         1175 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
        1266          805         1331          579          882          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
           2          186          219          181          399          205 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         106          104 

  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 
              88.0              543.5 
[1] "10.0 - 1636.0 (88.0)" "2.0 - 5925.0 (543.5)"
[1] "hr="     "9200000"
D18V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED         3        1         2        1
  10P GAIN WILD-TYPE     134       15        41       12
D18V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  3                134
  STAGE II                 1                 15
  STAGE III                2                 41
  STAGE IV                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  10P GAIN MUTATED     4   1     3
  10P GAIN WILD-TYPE 142  21    48
D18V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                   4                142
  T2                   1                 21
  T3+T4                3                 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
  10P GAIN MUTATED    2  1  0
  10P GAIN WILD-TYPE 37 19  4
D18V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                2                 37
  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  82   7 111
D18V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                6                 82
  M1                1                  7
  MX                1                111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     3   5
  10P GAIN WILD-TYPE  60 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3    5
  10P GAIN WILD-TYPE   60  153
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                3                 60
  MALE                  5                153
[1] 2 2
[1] FALSE
D18V8, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 55 
        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-A8LB         TCGA-G7-A8LC 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         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-A7SR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SX-A7SU 
"10P GAIN WILD-TYPE" 
D18V9, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 34 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-A44B         TCGA-B9-A69E 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-A8LB         TCGA-G7-A8LD 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-7773         TCGA-GL-A59T 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-HE-A5NK         TCGA-IA-A40U         TCGA-IA-A83S 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IZ-A6M8         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-SX-A7SR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-Y8-A894         TCGA-Y8-A896 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ 
"10P GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0     2
  10P GAIN WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           2     2
  10P GAIN WILD-TYPE                        50   145
D18V10, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                       2                 50
  WHITE                                           2                145
[1] 4 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   9 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0    6
  10P GAIN WILD-TYPE    9  169
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                6                169
[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 181   7
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 6                188 
  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         1469 

$`10Q GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 
          27            7           49            2          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
         516         1968            2          118           87            4 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
        1778          412          923          763         1357           26 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
          67          595          223          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         803          627           14          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          452          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-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-A7VF 
        1670         1040          578          757           97            7 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          13          208         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
         765          446          786          194          197          262 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
        1967         1965         5925          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
          32          378          546           27          341          140 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
        2072          408          360         1726         2228          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 
         376            4          364          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         541          493          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
        2816          391          540          428         1457         1443 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1005          876          823         1973          578         1175 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
        1266          805         1331          579          882          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
           2          186          219          181          399          205 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         106          104 

  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 
              88.0              543.5 
[1] "10.0 - 1636.0 (88.0)" "2.0 - 5925.0 (543.5)"
[1] "hr="     "9200000"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED         3        1         2        1
  10Q GAIN WILD-TYPE     134       15        41       12
D19V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  3                134
  STAGE II                 1                 15
  STAGE III                2                 41
  STAGE IV                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  10Q GAIN MUTATED     4   1     3
  10Q GAIN WILD-TYPE 142  21    48
D19V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                   4                142
  T2                   1                 21
  T3+T4                3                 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
  10Q GAIN MUTATED    2  1  0
  10Q GAIN WILD-TYPE 37 19  4
D19V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                2                 37
  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  82   7 111
D19V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                6                 82
  M1                1                  7
  MX                1                111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3   5
  10Q GAIN WILD-TYPE  60 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    5
  10Q GAIN WILD-TYPE   60  153
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                3                 60
  MALE                  5                153
[1] 2 2
[1] FALSE
D19V8, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 55 
        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-A8LB         TCGA-G7-A8LC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         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-A7SR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SX-A7SU 
"10Q GAIN WILD-TYPE" 
D19V9, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 34 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-A44B         TCGA-B9-A69E 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-A8LB         TCGA-G7-A8LD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-7773         TCGA-GL-A59T 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HE-A5NK         TCGA-IA-A40U         TCGA-IA-A83S 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IZ-A6M8         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-SX-A7SR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-Y8-A894         TCGA-Y8-A896 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ 
"10Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     2
  10Q GAIN WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           2     2
  10Q GAIN WILD-TYPE                        50   145
D19V10, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                       2                 50
  WHITE                                           2                145
[1] 4 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   9 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    6
  10Q GAIN WILD-TYPE    9  169
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                6                169
[1] 2 2
[1] FALSE

Clustering(20) Variable = 11P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     8   0
  11P GAIN WILD-TYPE 179   7
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 8                186 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                  7 
$`11P GAIN MUTATED`
TCGA-A4-A57E TCGA-AL-A5DJ TCGA-B9-4117 TCGA-BQ-5892 TCGA-F9-A7Q0 TCGA-G7-A8LC 
        1968           26           14          364           10          262 
TCGA-GL-7966 TCGA-P4-A5EB 
         112         2584 

$`11P GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
         379          516            2          118           87            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
          67          595          223          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         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-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
          64          585          207            5          452          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-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-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-A7VF TCGA-F9-A8NY 
        1040          578          757           97            7           36 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          13          208         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
         765          446          786          194          197         1967 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        1965         5925          393          841           32          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
         546           27          341          140         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         360         1726         2228          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          376            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         364          885          161         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
         841          616           11          369          541          493 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
         148         3035         2653         2816          391          540 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
         428         1457         1443         1005          876          823 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
        1973          578         1175         1266          805         1469 
TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
        1331          579          882          224            2          186 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         219          181          399          205          106          104 

  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 
               187                550 
[1] "10.0 - 2584.0 (187.0)" "2.0 - 5925.0 (550.0)" 
[1] "hr="     "2.7e+07"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED         4        0         3        2
  11P GAIN WILD-TYPE     133       16        40       11
D20V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  4                133
  STAGE II                 0                 16
  STAGE III                3                 40
  STAGE IV                 2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  11P GAIN MUTATED     4   2     4
  11P GAIN WILD-TYPE 142  20    47
D20V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                   4                142
  T2                   2                 20
  T3+T4                4                 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
  11P GAIN MUTATED    2  3  0
  11P GAIN WILD-TYPE 37 17  4
D20V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0                2                 37
  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   5
  11P GAIN WILD-TYPE  86   6 107
D20V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                2                 86
  M1                2                  6
  MX                5                107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     5   5
  11P GAIN WILD-TYPE  58 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5    5
  11P GAIN WILD-TYPE   58  153
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                5                 58
  MALE                  5                153
[1] 2 2
[1] FALSE
D20V8, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 54 
        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-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40X         TCGA-IA-A40Y 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-J7-8537         TCGA-Q2-A5QZ         TCGA-SX-A71R 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A71V 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SX-A7SO         TCGA-SX-A7SP         TCGA-SX-A7SQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SX-A7SR         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                 33 
        TCGA-A4-A48D         TCGA-A4-A5Y0         TCGA-B1-A654 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B9-A44B         TCGA-B9-A69E         TCGA-F9-A97G 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A59T         TCGA-GL-A9DD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-HE-A5NK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A83S         TCGA-IZ-A6M8 
"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-A7SR         TCGA-SX-A7SS         TCGA-WN-A9G9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     1
  11P GAIN WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           1     8
  11P GAIN WILD-TYPE                        51   139
D20V10, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       1                 51
  WHITE                                           8                139
[1] 4 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   9 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   10
  11P GAIN WILD-TYPE    9  165
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               10                165
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED     9   0
  11Q GAIN WILD-TYPE 178   7
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 9                185 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 0                  7 
$`11Q GAIN MUTATED`
TCGA-A4-A57E TCGA-AL-A5DJ TCGA-B9-4117 TCGA-BQ-5892 TCGA-F9-A7Q0 TCGA-G7-A8LC 
        1968           26           14          364           10          262 
TCGA-GL-7966 TCGA-P4-A5EB TCGA-Q2-A5QZ 
         112         2584          428 

$`11Q GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
         379          516            2          118           87            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
          67          595          223          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         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-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
          64          585          207            5          452          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-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-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-A7VF TCGA-F9-A8NY 
        1040          578          757           97            7           36 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          13          208         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
         765          446          786          194          197         1967 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        1965         5925          393          841           32          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
         546           27          341          140         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         360         1726         2228          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          376            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         364          885          161         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
         841          616           11          369          541          493 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
         148         3035         2653         2816          391          540 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1457         1443         1005          876          823         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
         578         1175         1266          805         1469         1331 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
         579          882          224            2          186          219 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         181          399          205          106          104 

  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 
               262                554 
[1] "10.0 - 2584.0 (262.0)" "2.0 - 5925.0 (554.0)" 
[1] "hr="     "2.7e+07"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         4        0         4        1
  11Q GAIN WILD-TYPE     133       16        39       12
D21V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  4                133
  STAGE II                 0                 16
  STAGE III                4                 39
  STAGE IV                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  11Q GAIN MUTATED     4   2     4
  11Q GAIN WILD-TYPE 142  20    47
D21V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                   4                142
  T2                   2                 20
  T3+T4                4                 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
  11Q GAIN MUTATED    2  2  0
  11Q GAIN WILD-TYPE 37 18  4
D21V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                2                 37
  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   6
  11Q GAIN WILD-TYPE  86   7 106
D21V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                2                 86
  M1                1                  7
  MX                6                106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     6   4
  11Q GAIN WILD-TYPE  57 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      6    4
  11Q GAIN WILD-TYPE   57  154
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                6                 57
  MALE                  4                154
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     1
  11Q GAIN WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           2     7
  11Q GAIN WILD-TYPE                        50   140
D21V10, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       2                 50
  WHITE                                           7                140
[1] 4 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  10
  11Q GAIN WILD-TYPE   9 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   10
  11Q GAIN WILD-TYPE    9  165
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               10                165
[1] 2 2
[1] FALSE

Clustering(22) Variable = 12P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    75   5
  12P GAIN WILD-TYPE 112   2
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                80                114 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 5                  2 
$`12P GAIN MUTATED`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
         207          554          582            2          140          780 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A6HP 
          23          597          600          516            2            4 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-7173 TCGA-B1-A47N TCGA-B1-A656 TCGA-B3-3925 
        1636          412         1357          747           14         1029 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
         309         1536          857           35         1338          671 
TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5877 TCGA-BQ-5887 TCGA-BQ-5891 
         585            5          167          270          771           29 
TCGA-BQ-5892 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7837 
         364          232          218          116          414         1142 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-F9-A7Q0 
         114          445         1240         2460         1856           10 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
          36          208         1194          194          197          262 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
        1967         5925          112           32          378          546 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          27          341         2072          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         511           62          364          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 TCGA-MH-A854 TCGA-P4-A5EB TCGA-PJ-A5Z8 
         845          924          616           11         2584          391 
TCGA-PJ-A5Z9 TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SQ TCGA-SX-A7SR 
         540         1005          876         1973         1266          805 
TCGA-SX-A7SS TCGA-Y8-A8RY 
        1469          399 

$`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-A57E TCGA-A4-A5Y0 
         729          709          436          379         1968          118 
TCGA-A4-A5Y1 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-A5DJ TCGA-AT-A5NU 
          87         1778          923          763           26           67 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
         595          223          659          513          108          510 
TCGA-B1-A657 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 
         200          307          930         1049          379          803 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A69E 
         627           14          460           64          207          452 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
          52         2639          586         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5894 
         792          921          792          403          233           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-7060 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 
         799          612          214          353         3950         1093 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5901 
         744          419           92         2429         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6790 
         578          757           97            7           13         1575 
TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LE 
        1479         1059          765          446          786         1965 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40X 
         393          841          140          408         2228          608 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A561 
         677          649          146          376            4          841 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5ED TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A7SL TCGA-SX-A7SN 
        2816          428         1457         1443          823          578 
TCGA-SX-A7SO TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
        1175         1331          579          882          224            2 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         186          219          181          205          106          104 

  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 
             478.0              578.5 
[1] "2.0 - 5925.0 (478.0)" "2.0 - 3950.0 (578.5)"
[1] "hr=" "4.1"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED        58        7        12        8
  12P GAIN WILD-TYPE      79        9        31        5
D22V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                 58                 79
  STAGE II                 7                  9
  STAGE III               12                 31
  STAGE IV                 8                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  12P GAIN MUTATED   61  8    20
  12P GAIN WILD-TYPE 85 14    31
D22V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                  61                 85
  T2                   8                 14
  T3+T4               20                 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
  12P GAIN MUTATED   13  9  2
  12P GAIN WILD-TYPE 26 11  2
D22V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               13                 26
  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   30  4 51
  12P GAIN WILD-TYPE 58  4 61
D22V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               30                 58
  M1                4                  4
  MX               51                 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"
D22V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   17 74
  12P GAIN WILD-TYPE 46 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     17   74
  12P GAIN WILD-TYPE   46   84
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               17                 46
  MALE                 74                 84
[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     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                          22    60
  12P GAIN WILD-TYPE                        30    87
D22V10, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                      22                 30
  WHITE                                          60                 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"
D22V11, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    1 78
  12P GAIN WILD-TYPE  8 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   78
  12P GAIN WILD-TYPE    8   97
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               78                 97
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    75   5
  12Q GAIN WILD-TYPE 112   2
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                80                114 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                  2 
$`12Q GAIN MUTATED`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
         207          554          582            2          140          780 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A6HP 
          23          597          600          516            2            4 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-7173 TCGA-B1-A47N TCGA-B1-A656 TCGA-B3-3925 
        1636          412         1357          747           14         1029 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
         309         1536          857           35         1338          671 
TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5877 TCGA-BQ-5887 TCGA-BQ-5891 
         585            5          167          270          771           29 
TCGA-BQ-5892 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7837 
         364          232          218          116          414         1142 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-F9-A7Q0 
         114          445         1240         2460         1856           10 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
          36          208         1194          194          197          262 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
        1967         5925          112           32          378          546 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          27          341         2072          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         511           62          364          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 TCGA-MH-A854 TCGA-P4-A5EB TCGA-PJ-A5Z8 
         845          924          616           11         2584          391 
TCGA-PJ-A5Z9 TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SQ TCGA-SX-A7SR 
         540         1005          876         1973         1266          805 
TCGA-SX-A7SS TCGA-Y8-A8RY 
        1469          399 

$`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-A57E TCGA-A4-A5Y0 
         729          709          436          379         1968          118 
TCGA-A4-A5Y1 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-A5DJ TCGA-AT-A5NU 
          87         1778          923          763           26           67 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
         595          223          659          513          108          510 
TCGA-B1-A657 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 
         200          307          930         1049          379          803 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A69E 
         627           14          460           64          207          452 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
          52         2639          586         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5894 
         792          921          792          403          233           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-7060 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 
         799          612          214          353         3950         1093 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5901 
         744          419           92         2429         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6790 
         578          757           97            7           13         1575 
TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LE 
        1479         1059          765          446          786         1965 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40X 
         393          841          140          408         2228          608 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A561 
         677          649          146          376            4          841 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5ED TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A7SL TCGA-SX-A7SN 
        2816          428         1457         1443          823          578 
TCGA-SX-A7SO TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
        1175         1331          579          882          224            2 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         186          219          181          205          106          104 

  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 
             478.0              578.5 
[1] "2.0 - 5925.0 (478.0)" "2.0 - 3950.0 (578.5)"
[1] "hr=" "4.1"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED        58        7        12        8
  12Q GAIN WILD-TYPE      79        9        31        5
D23V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                 58                 79
  STAGE II                 7                  9
  STAGE III               12                 31
  STAGE IV                 8                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  12Q GAIN MUTATED   61  8    20
  12Q GAIN WILD-TYPE 85 14    31
D23V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                  61                 85
  T2                   8                 14
  T3+T4               20                 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
  12Q GAIN MUTATED   13  9  2
  12Q GAIN WILD-TYPE 26 11  2
D23V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               13                 26
  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   30  4 51
  12Q GAIN WILD-TYPE 58  4 61
D23V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               30                 58
  M1                4                  4
  MX               51                 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"
D23V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   17 74
  12Q GAIN WILD-TYPE 46 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     17   74
  12Q GAIN WILD-TYPE   46   84
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               17                 46
  MALE                 74                 84
[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     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                          22    60
  12Q GAIN WILD-TYPE                        30    87
D23V10, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                      22                 30
  WHITE                                          60                 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"
D23V11, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    1 78
  12Q GAIN WILD-TYPE  8 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   78
  12Q GAIN WILD-TYPE    8   97
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               78                 97
[1] 2 2
[1] FALSE

Clustering(24) Variable = 13Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    19   1
  13Q GAIN WILD-TYPE 168   6
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                20                174 
  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          578 
TCGA-SX-A7SQ TCGA-Y8-A897 
        1266          219 

$`13Q GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          780 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
         709           23          597          379          516         1968 
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-B1-7332 TCGA-B1-A47M 
         923          763         1357           26          223          659 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         747          513          108          510           14          200 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-A6W5 TCGA-B9-4113 
        1029          307          930         1049          309         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         857          803          627          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          452          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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 
        1242          792          792          771          403          233 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 
          29          364           84         3760         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-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
          97           10            7           36           13          208 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
        1479         1194          765          446          786          194 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         197          262         1967         1965         5925          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
         112          841           32          378          546           27 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         341          140         2072          408          360         1726 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        2228          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          376            4          364          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          845          924          841          616 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
          11          369          493          148         3035         2653 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
        2816          391          540          428         1457         1443 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SR 
        1005          876          823         1973         1175          805 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
        1469         1331          579          882          224            2 
TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         186          181          399          205          106          104 

  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 
             586.5              514.5 
[1] "14.0 - 2948.0 (586.5)" "2.0 - 5925.0 (514.5)" 
[1] "hr=" "1.3"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED        16        0         5        0
  13Q GAIN WILD-TYPE     121       16        38       13
D24V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                 16                121
  STAGE II                 0                 16
  STAGE III                5                 38
  STAGE IV                 0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  13Q GAIN MUTATED    18   1     4
  13Q GAIN WILD-TYPE 128  21    47
D24V4, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                  18                128
  T2                   1                 21
  T3+T4                4                 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
  13Q GAIN MUTATED    3  2  0
  13Q GAIN WILD-TYPE 36 18  4
D24V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0                3                 36
  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  12
  13Q GAIN WILD-TYPE  78   8 100
D24V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0               10                 78
  M1                0                  8
  MX               12                100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     7  16
  13Q GAIN WILD-TYPE  56 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      7   16
  13Q GAIN WILD-TYPE   56  142
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                7                 56
  MALE                 16                142
[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                 33 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-A44B         TCGA-B9-A69E 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-A8LB         TCGA-G7-A8LD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-7773         TCGA-GL-A59T 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HE-A5NK         TCGA-IA-A40U         TCGA-IA-A83S 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IZ-A6M8         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-A7SR         TCGA-SX-A7SS         TCGA-WN-A9G9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RZ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     0
  13Q GAIN WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           4    18
  13Q GAIN WILD-TYPE                        48   129
D24V10, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       4                 48
  WHITE                                          18                129
[1] 4 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  18
  13Q GAIN WILD-TYPE   7 157
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2   18
  13Q GAIN WILD-TYPE    7  157
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               18                157
[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 186   7
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                193 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 0                  7 
$`14Q GAIN MUTATED`
TCGA-GL-7966 
         112 

$`14Q GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         379          516         1968            2          118           87 
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-B1-7332 TCGA-B1-A47M 
        1357           26           67          595          223          659 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         747          513          108          510           14          200 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379          309 
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          452          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-F9-A97G 
         757           97           10            7           36           13 
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-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
         446          786          194          197          262         1967 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        1965         5925          393          841           32          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
         546           27          341          140         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         360         1726         2228          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          376            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         364          885          161         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
         841          616           11          369          541          493 
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 
         540          428         1457         1443         1005          876 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR 
         823         1973          578         1175         1266          805 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
        1469         1331          579          882          224            2 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
         186          219          181          399          205          106 
TCGA-Y8-A8S1 
         104 

  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                541 
[1] "112.0 - 112.0 (112.0)" "2.0 - 5925.0 (541.0)" 
[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                214 
        TCGA-2K-A9WE         TCGA-A4-7286         TCGA-A4-7287 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7288         TCGA-A4-7583         TCGA-A4-7584 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7585         TCGA-A4-7732         TCGA-A4-7734 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7828         TCGA-A4-7915         TCGA-A4-7996 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7997         TCGA-A4-8098         TCGA-A4-8310 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8515 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-8516         TCGA-A4-8517         TCGA-A4-8518 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A48D         TCGA-A4-A4ZT 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5DU         TCGA-A4-A5XZ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A5Y0         TCGA-A4-A5Y1         TCGA-A4-A6HP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A772         TCGA-AL-3466         TCGA-AL-3467 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-AL-A5DJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AT-A5NU         TCGA-B1-5398         TCGA-B1-7332 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-A47M         TCGA-B1-A47N         TCGA-B1-A47O 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-A654         TCGA-B1-A655         TCGA-B1-A656 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-A657         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-F9-A97G 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-6796 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LB         TCGA-G7-A8LC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-GL-6846 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-8500         TCGA-GL-A4EM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-A59R         TCGA-GL-A59T         TCGA-GL-A9DC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-GL-A9DE         TCGA-HE-A5NF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HE-A5NH         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HE-A5NK         TCGA-HE-A5NL         TCGA-IA-A40U 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IA-A40X         TCGA-IA-A40Y         TCGA-IA-A83S 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IA-A83T         TCGA-IA-A83W         TCGA-IZ-8195 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IZ-8196         TCGA-IZ-A6M8         TCGA-IZ-A6M9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537         TCGA-KV-A6GD 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KV-A6GE         TCGA-KV-A74V         TCGA-MH-A55W 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A55Z         TCGA-MH-A560         TCGA-MH-A561 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A562         TCGA-MH-A854         TCGA-MH-A855 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A856         TCGA-MH-A857         TCGA-O9-A75Z 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-A5E7         TCGA-P4-A5E8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P4-A5EA         TCGA-P4-A5EB         TCGA-P4-A5ED 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9         TCGA-Q2-A5QZ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A71S         TCGA-SX-A71U 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A71V         TCGA-SX-A7SL         TCGA-SX-A7SM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SN         TCGA-SX-A7SO         TCGA-SX-A7SP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SQ         TCGA-SX-A7SR         TCGA-SX-A7SS 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SU         TCGA-Y8-A894         TCGA-Y8-A895 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A897         TCGA-Y8-A898 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RY         TCGA-Y8-A8RZ         TCGA-Y8-A8S0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A8S1 
"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     137       16        40       13
D25V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  0                137
  STAGE II                 0                 16
  STAGE III                3                 40
  STAGE IV                 0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  14Q GAIN MUTATED     0   0     3
  14Q GAIN WILD-TYPE 146  22    48
D25V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                   0                146
  T2                   0                 22
  T3+T4                3                 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
  14Q GAIN MUTATED    0  2  0
  14Q GAIN WILD-TYPE 39 18  4
D25V5, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                 61 
        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-A47O         TCGA-B1-A655 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-A656         TCGA-B1-A657         TCGA-B9-7268 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5885         TCGA-BQ-5887 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7045         TCGA-BQ-7048 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7056 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-DW-7963         TCGA-DZ-6131 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F9-A8NY         TCGA-F9-A97G         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-GL-A9DC         TCGA-IA-A40U         TCGA-IA-A40Y 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IA-A83W         TCGA-J7-6720         TCGA-J7-8537 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KV-A74V         TCGA-P4-A5E6         TCGA-P4-A5E8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-P4-A5EA         TCGA-SX-A71R         TCGA-SX-A7SM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SS         TCGA-Y8-A897 
"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  86   8 111
D25V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                2                 86
  M1                0                  8
  MX                1                111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2   1
  14Q GAIN WILD-TYPE  61 157
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2    1
  14Q GAIN WILD-TYPE   61  157
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                2                 61
  MALE                  1                157
[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     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           0     2
  14Q GAIN WILD-TYPE                        52   145
D25V10, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                204 
        TCGA-2K-A9WE         TCGA-A4-7286         TCGA-A4-7287 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7288         TCGA-A4-7583         TCGA-A4-7584 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7585         TCGA-A4-7732         TCGA-A4-7734 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7828         TCGA-A4-7915         TCGA-A4-7996 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-7997         TCGA-A4-8098         TCGA-A4-8310 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8515 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-8516         TCGA-A4-8517         TCGA-A4-8518 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A48D         TCGA-A4-A4ZT 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5DU         TCGA-A4-A5XZ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A5Y0         TCGA-A4-A5Y1         TCGA-A4-A6HP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A4-A772         TCGA-AL-3466         TCGA-AL-3467 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-AL-A5DJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AT-A5NU         TCGA-B1-5398         TCGA-B1-7332 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-A47M         TCGA-B1-A47N         TCGA-B1-A47O 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-A654         TCGA-B1-A655         TCGA-B1-A656 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B1-A657         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-F9-A97G         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-A8LB         TCGA-G7-A8LC         TCGA-G7-A8LD 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G7-A8LE         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-GL-A9DC         TCGA-GL-A9DD 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GL-A9DE         TCGA-IA-A40U         TCGA-IA-A40X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IA-A83S         TCGA-IA-A83T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IA-A83W         TCGA-IZ-8195         TCGA-IZ-8196 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IZ-A6M8         TCGA-IZ-A6M9         TCGA-J7-6720 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-J7-8537         TCGA-KV-A6GD         TCGA-KV-A6GE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-KV-A74V         TCGA-MH-A55W         TCGA-MH-A55Z 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A560         TCGA-MH-A561         TCGA-MH-A562 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A855         TCGA-MH-A856 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MH-A857         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-A7SR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-WN-A9G9         TCGA-WN-AB4C 
"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-A897         TCGA-Y8-A898         TCGA-Y8-A8RY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-Y8-A8S0         TCGA-Y8-A8S1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
D25V11, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0   1
  14Q GAIN WILD-TYPE   9 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0    1
  14Q GAIN WILD-TYPE    9  174
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                1                174
[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 182   7
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                189 
  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          428 

$`15Q GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         379          516         1968            2          118           87 
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-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
        1357           67          595          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         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          452 
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-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         403          233           29           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-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
           7           36           13          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          194 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         197          262         1967         1965         5925          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
         112          841           32          378          546           27 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         341          140         2072          408          360         1726 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        2228          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          376            4          364          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          845          924          841          616 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
          11          369          541          493          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
        2653         2816          391          540         1457         1443 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1005          876          823         1973          578         1175 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C 
        1266          805         1469         1331          579          882 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
         224            2          186          219          181          399 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         205          106          104 

  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 
               364                546 
[1] "26.0 - 2584.0 (364.0)" "2.0 - 5925.0 (546.0)" 
[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     135       15        41       13
D26V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  2                135
  STAGE II                 1                 15
  STAGE III                2                 41
  STAGE IV                 0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  15Q GAIN MUTATED     2   1     2
  15Q GAIN WILD-TYPE 144  21    49
D26V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                   2                144
  T2                   1                 21
  T3+T4                2                 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
  15Q GAIN MUTATED    1  0  0
  15Q GAIN WILD-TYPE 38 20  4
D26V5, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 62 
        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-A47O         TCGA-B1-A655 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B1-A656         TCGA-B1-A657         TCGA-B9-7268 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5882         TCGA-BQ-5885 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5893 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7045         TCGA-BQ-7048 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7056 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-DW-7963         TCGA-DZ-6131 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F9-A8NY         TCGA-F9-A97G         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-GL-A9DC         TCGA-IA-A40U 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IA-A83W         TCGA-J7-6720 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-J7-8537         TCGA-KV-A74V         TCGA-P4-A5E6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-P4-A5E8         TCGA-P4-A5EA         TCGA-SX-A71R 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SP         TCGA-SX-A7SS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-Y8-A897         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  87   8 108
D26V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                1                 87
  M1                0                  8
  MX                4                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     3   2
  15Q GAIN WILD-TYPE  60 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    2
  15Q GAIN WILD-TYPE   60  156
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                3                 60
  MALE                  2                156
[1] 2 2
[1] FALSE
D26V8, continuous
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 55 
        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-A8LB         TCGA-G7-A8LC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         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-A7SR         TCGA-SX-A7SS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-SX-A7SU 
"15Q GAIN WILD-TYPE" 
D26V9, continuous
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 33 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-A44B         TCGA-B9-A69E 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-A8LB         TCGA-G7-A8LD 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-7773         TCGA-GL-A59T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HE-A5NK         TCGA-IA-A40U         TCGA-IA-A83S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IZ-A6M8         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-A7SR         TCGA-SX-A7SS         TCGA-WN-A9G9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RZ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     0
  15Q GAIN WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           2     3
  15Q GAIN WILD-TYPE                        50   144
D26V10, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       2                 50
  WHITE                                           3                144
[1] 4 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   9 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    5
  15Q GAIN WILD-TYPE    9  170
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                5                170
[1] 2 2
[1] FALSE

Clustering(27) Variable = 16P GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED   100   2
  16P GAIN WILD-TYPE  87   5
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               102                 92 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                  5 
$`16P GAIN MUTATED`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7996 TCGA-A4-7997 
         207          554          493            3           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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y1 
         436          379          516         1968            2           87 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A657 
        1636          412           67          595          659          200 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 
         930          379          309          857           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-A8YI TCGA-BQ-5875 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 
          52         2639         1454          792          771          233 
TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7060 TCGA-BQ-7062 
          29         3760         2948         1533          214          116 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6134 TCGA-EV-5902 
        3950         1093          744         1240         1856          578 
TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
         757           10            7           36           13          208 
TCGA-G7-6790 TCGA-G7-6797 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-6846 TCGA-GL-7966 
        1575          765          197          262         5925          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF 
         841           32          546           27          341         2072 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 
         360         1726          167          511           62          677 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         146          376          364          885          161         1043 
TCGA-MH-A560 TCGA-MH-A854 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-PJ-A5Z9 
         924           11         3035         2653         2584          540 
TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SQ 
        1457         1005          876          823          578         1266 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8S0 
         805         1469            2          219          181          106 

$`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-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          747          513          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          452          167          586          270         1938 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-5894 
        1242          792          921          403          364           84 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        2839         1864         1516          799          612          232 
TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 
         218          353          414         1142          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 
         445           92         2429         2460         1670         1040 
TCGA-F9-A4JJ TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 
          97         1479         1194         1059          446          786 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-A59R TCGA-GL-A9DE 
         194         1967         1965          393          378          140 
TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40X TCGA-IZ-8196 TCGA-J7-8537 TCGA-MH-A55Z 
         408         2228          608          649            4          845 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
         841          616          369          541          493          148 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71S TCGA-SX-A7SM TCGA-SX-A7SO 
        2816          391          428         1443         1973         1175 
TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8RY 
        1331          579          882          224          186          399 
TCGA-Y8-A8RZ TCGA-Y8-A8S1 
         205          104 

  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 
               543                527 
[1] "2.0 - 5925.0 (543.0)" "4.0 - 2839.0 (527.0)"
[1] "hr=" "2.8"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED        72        8        24        6
  16P GAIN WILD-TYPE      65        8        19        7
D27V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                 72                 65
  STAGE II                 8                  8
  STAGE III               24                 19
  STAGE IV                 6                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  16P GAIN MUTATED   78 13    25
  16P GAIN WILD-TYPE 68  9    26
D27V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                  78                 68
  T2                  13                  9
  T3+T4               25                 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   20 10  2
  16P GAIN WILD-TYPE 19 10  2
D27V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               20                 19
  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   45  3 61
  16P GAIN WILD-TYPE 43  5 51
D27V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0               45                 43
  M1                3                  5
  MX               61                 51
[1] 3 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   24 93
  16P GAIN WILD-TYPE 39 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     24   93
  16P GAIN WILD-TYPE   39   65
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               24                 39
  MALE                 93                 65
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  2     3
  16P GAIN WILD-TYPE                                0     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                          19    86
  16P GAIN WILD-TYPE                        33    61
D27V10, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           3                  2
  BLACK OR AFRICAN AMERICAN                      19                 33
  WHITE                                          86                 61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    2 96
  16P GAIN WILD-TYPE  7 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2   96
  16P GAIN WILD-TYPE    7   79
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               96                 79
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16Q GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   99  1
  16Q GAIN WILD-TYPE 88  6
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               100                 94 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                  6 
$`16Q GAIN MUTATED`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7996 TCGA-A4-7997 
         207          554          493            3           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-A57E TCGA-A4-A5XZ TCGA-AL-3468 
         436          379          516         1968            2         1636 
TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-4103 
         412           67          595          659          200          930 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
         379          309          857           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YI 
        1338          671           64          585            5           52 
TCGA-BQ-5875 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-7044 
        2639         1454          792          771           29         3760 
TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7834 TCGA-DW-7836 
        2948         1533          214          116         3950         1093 
TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6134 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 
         744         1240         1856          578          757           10 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6797 
           7           36           13          208         1575          765 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
         197          262         5925          112          841           32 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NL 
         546           27          341         2072          360          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         511          608           62          677          146          376 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A560 TCGA-MH-A854 
         364          885          161         1043          924           11 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71U 
        3035         2653         2584          540         1457         1005 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
         876          823          578         1266          805         1469 
TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8S0 
           2          219          181          106 

$`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-A47O TCGA-B1-A654 TCGA-B1-A655 
          26          223          747          513          108          510 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4115 
          14         1029          307         1049         1536          803 
TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-BQ-5876 TCGA-BQ-5877 
         627          207          452          167          586          270 
TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5890 
        1938         1242          792          921          403          233 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 
         364           84         2839         1864         1516          799 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 
         612          232          218          353          414         1142 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
         419          114          445           92         2429         2460 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-F9-A4JJ TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
        1670         1040           97         1479         1194         1059 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-7773 
         446          786          194         1967         1965          393 
TCGA-GL-A59R TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IZ-8196 
         378          140          408         1726         2228          649 
TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A855 TCGA-MH-A856 
           4          845          841          616          369          541 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71S 
         493          148         2816          391          428         1443 
TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
        1973         1175         1331          579          882          224 
TCGA-Y8-A896 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S1 
         186          399          205          104 

  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 
             550.0              511.5 
[1] "2.0 - 5925.0 (550.0)" "4.0 - 2839.0 (511.5)"
[1] "hr=" "6.5"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED        73        8        21        5
  16Q GAIN WILD-TYPE      64        8        22        8
D28V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                 73                 64
  STAGE II                 8                  8
  STAGE III               21                 22
  STAGE IV                 5                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  16Q GAIN MUTATED   77 13    22
  16Q GAIN WILD-TYPE 69  9    29
D28V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                  77                 69
  T2                  13                  9
  T3+T4               22                 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   19  8  1
  16Q GAIN WILD-TYPE 20 12  3
D28V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               19                 20
  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   42  2 61
  16Q GAIN WILD-TYPE 46  6 51
D28V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0               42                 46
  M1                2                  6
  MX               61                 51
[1] 3 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   25 88
  16Q GAIN WILD-TYPE 38 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     25   88
  16Q GAIN WILD-TYPE   38   70
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               25                 38
  MALE                 88                 70
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  2     3
  16Q GAIN WILD-TYPE                                0     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                          20    82
  16Q GAIN WILD-TYPE                        32    65
D28V10, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           3                  2
  BLACK OR AFRICAN AMERICAN                      20                 32
  WHITE                                          82                 65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    2 93
  16Q GAIN WILD-TYPE  7 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2   93
  16Q GAIN WILD-TYPE    7   82
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               93                 82
[1] 2 2
[1] FALSE

Clustering(29) Variable = 17P GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED   120   3
  17P GAIN WILD-TYPE  67   4
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               123                 71 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                  4 
$`17P GAIN MUTATED`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 
         207          554          493          582           27           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-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 
         747          108          200         1029          930          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
         309         1536          857          803           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH 
         460         1338          671          585            5          167 
TCGA-BQ-5881 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7051 
        1454          771           29          364         2948         1533 
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-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF 
        1240         1856         1040          757           10            7 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 
          36          208         1575         1194         1059          786 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
         194          197          262         1967         1965         5925 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
         112           32          378          546           27          341 
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-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
          62          677          649          146          376            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         364          885          161         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-PJ-A5Z9 
         841          616          148         2653         2584          540 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN 
         428         1457         1443         1005          876          578 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-AB4C TCGA-Y8-A895 
        1266          805         1469         1331          882            2 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
         181          399          106 

$`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-A57E TCGA-A4-A5Y1 TCGA-AL-3467 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
        1968           87         1778          763         1357          595 
TCGA-B1-A47O TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 
         513          510           14          307         1049          627 
TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
          64          207          452           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
         270         1938         1242          792          921          792 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 
         403          233           84         3760         2839         1864 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6131 
        1516          799          612          232          218         2429 
TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A97G TCGA-G7-6792 
        2460         1670          578           97           13         1479 
TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A9DE TCGA-HE-A5NK 
         765          446          393          841          140         2228 
TCGA-IA-A40X TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E6 
         608           11          369          541          493         3035 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-WN-A9G9 
        2816          391          823         1973         1175          579 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
         224          186          219          205          104 

  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 
               540                541 
[1] "2.0 - 5925.0 (540.0)" "2.0 - 3760.0 (541.0)"
[1] "hr=" "1.6"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P GAIN MUTATED        96        9        16        5
  17P GAIN WILD-TYPE      41        7        27        8
D29V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                 96                 41
  STAGE II                 9                  7
  STAGE III               16                 27
  STAGE IV                 5                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  17P GAIN MUTATED   99 14    21
  17P GAIN WILD-TYPE 47  8    30
D29V4, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                  99                 47
  T2                  14                  8
  T3+T4               21                 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
  17P GAIN MUTATED   18  8  1
  17P GAIN WILD-TYPE 21 12  3
D29V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               18                 21
  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
  17P GAIN MUTATED   42  2 81
  17P GAIN WILD-TYPE 46  6 31
D29V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0               42                 46
  M1                2                  6
  MX               81                 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"
D29V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    33 102
  17P GAIN WILD-TYPE  30  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     33  102
  17P GAIN WILD-TYPE   30   56
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               33                 30
  MALE                102                 56
[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     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                          28    93
  17P GAIN WILD-TYPE                        24    54
D29V10, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           4                  1
  BLACK OR AFRICAN AMERICAN                      28                 24
  WHITE                                          93                 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"
D29V11, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     4 116
  17P GAIN WILD-TYPE   5  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4  116
  17P GAIN WILD-TYPE    5   59
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO              116                 59
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17Q GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED   131   3
  17Q GAIN WILD-TYPE  56   4
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               134                 60 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                  4 
$`17Q GAIN MUTATED`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207          554          493          582           27            7 
TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
          49          780          729          709           23          597 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 
         600          436          516         1968            2          118 
TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-A5DJ TCGA-AT-A5NU 
           4         1636          412          923           26           67 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
         223          659          747          513          108          510 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
         200         1029          930          379          309         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-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5875 
         671           64          585            5          167         2639 
TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
        1454          792          771          403          233           29 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7060 TCGA-BQ-7062 
         364         2948         1533         1516          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-6132 
         419          114          445           92         1240         2460 
TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
        1856         1040          757           10            7           36 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM 
         208         1575         1194         1059          786          194 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 
         197          262         1967         1965         5925          112 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF 
          32          378          546           27          341         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y 
         408          360         1726          167          511           62 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
         677          649          146          376            4          364 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          845          924          841 
TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         616          148         2653         2584          540          428 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SQ 
        1457         1443         1005          876          578         1266 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-AB4C TCGA-Y8-A895 TCGA-Y8-A898 
         805         1469         1331          882            2          181 
TCGA-Y8-A8RY TCGA-Y8-A8S0 
         399          106 

$`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          452           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-F9-A97G 
         218         2429         1670          578           97           13 
TCGA-G7-6792 TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A9DE 
        1479          765          446          393          841          140 
TCGA-HE-A5NK TCGA-IA-A40X TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
        2228          608           11          369          541          493 
TCGA-P4-A5E6 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO 
        3035         2816          391          823         1973         1175 
TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
         579          224          186          219          205          104 

  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 
             528.0              559.5 
[1] "2.0 - 5925.0 (528.0)" "2.0 - 3760.0 (559.5)"
[1] "hr=" "2.4"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED       100       10        22        8
  17Q GAIN WILD-TYPE      37        6        21        5
D30V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                100                 37
  STAGE II                10                  6
  STAGE III               22                 21
  STAGE IV                 8                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  17Q GAIN MUTATED   103  16    29
  17Q GAIN WILD-TYPE  43   6    22
D30V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                 103                 43
  T2                  16                  6
  T3+T4               29                 22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  17Q GAIN MUTATED   24  9  3
  17Q GAIN WILD-TYPE 15 11  1
D30V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               24                 15
  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   49  4 85
  17Q GAIN WILD-TYPE 39  4 27
D30V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               49                 39
  M1                4                  4
  MX               85                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    40 109
  17Q GAIN WILD-TYPE  23  49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     40  109
  17Q GAIN WILD-TYPE   23   49
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               40                 23
  MALE                109                 49
[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     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                          31   103
  17Q GAIN WILD-TYPE                        21    44
D30V10, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           4                  1
  BLACK OR AFRICAN AMERICAN                      31                 21
  WHITE                                         103                 44
[1] 4 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     5 125
  17Q GAIN WILD-TYPE   4  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5  125
  17Q GAIN WILD-TYPE    4   50
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                  4
  NOT HISPANIC OR LATINO              125                 50
[1] 2 2
[1] FALSE

Clustering(31) Variable = 18P GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED     9   1
  18P GAIN WILD-TYPE 178   6
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                10                184 
  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-G7-A8LB TCGA-G7-A8LC TCGA-HE-A5NJ TCGA-SX-A7SS 
         197          262         1726         1469 

$`18P GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
         379          516         1968            2          118            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          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-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         513          108          510           14          200         1029 
TCGA-B3-3926 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
         307          379          309         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          452          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-5561 TCGA-DW-7834 TCGA-DW-7836 
         214          218          116          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-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
          13          208         1479         1194         1059          765 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
         446          786          194         1967         1965         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          378          546 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          27          341          140         2072          408          360 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        2228          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          376            4          364          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          845          924          841          616 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
          11          369          541          493          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2653         2584         2816          391          540          428 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1457         1443         1005          876          823         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SU TCGA-WN-A9G9 
         578         1175         1266          805         1331          579 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
         882          224            2          186          219          181 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         399          205          106          104 

  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 
             695.0              540.5 
[1] "87.0 - 1726.0 (695.0)" "2.0 - 5925.0 (540.5)" 
[1] "hr=" "3.9"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P GAIN MUTATED         5        1         2        2
  18P GAIN WILD-TYPE     132       15        41       11
D31V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  5                132
  STAGE II                 1                 15
  STAGE III                2                 41
  STAGE IV                 2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  18P GAIN MUTATED     7   2     2
  18P GAIN WILD-TYPE 139  20    49
D31V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                   7                139
  T2                   2                 20
  T3+T4                2                 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
  18P GAIN MUTATED    1  2  0
  18P GAIN WILD-TYPE 38 18  4
D31V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                1                 38
  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   4
  18P GAIN WILD-TYPE  83   7 108
D31V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                5                 83
  M1                1                  7
  MX                4                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     1  10
  18P GAIN WILD-TYPE  62 148
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   10
  18P GAIN WILD-TYPE   62  148
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                1                 62
  MALE                 10                148
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     0
  18P GAIN WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           0    10
  18P GAIN WILD-TYPE                        52   137
D31V10, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       0                 52
  WHITE                                          10                137
[1] 4 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  10
  18P GAIN WILD-TYPE   9 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   10
  18P GAIN WILD-TYPE    9  165
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               10                165
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18Q GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED     8   0
  18Q GAIN WILD-TYPE 179   7
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                186 
  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-G7-A8LB 
         930         1049          460          353         1575          197 
TCGA-G7-A8LC TCGA-SX-A7SS 
         262         1469 

$`18Q GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         379          516         1968            2          118           87 
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-B1-7332 TCGA-B1-A47M 
        1357           26           67          595          223          659 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         747          513          108          510           14          200 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
        1029          307          379          309         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
         803          627           14           35         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
          64          585          207            5          452          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-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-5561 TCGA-DW-7834 
         232          214          218          116          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-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          36           13          208         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE 
         765          446          786          194         1967         1965 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
         546           27          341          140         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         360         1726         2228          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          376            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         364          885          161         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
         841          616           11          369          541          493 
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 
         540          428         1457         1443         1005          876 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR 
         823         1973          578         1175         1266          805 
TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
        1331          579          882          224            2          186 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         219          181          399          205          106          104 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               197                  2 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              1575               5925 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             695.0              540.5 
[1] "197.0 - 1575.0 (695.0)" "2.0 - 5925.0 (540.5)"  
[1] "hr="     "2.6e+07"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED         5        1         1        1
  18Q GAIN WILD-TYPE     132       15        42       12
D32V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  5                132
  STAGE II                 1                 15
  STAGE III                1                 42
  STAGE IV                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  18Q GAIN MUTATED     5   2     1
  18Q GAIN WILD-TYPE 141  20    50
D32V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                   5                141
  T2                   2                 20
  T3+T4                1                 50
[1] 3 2
[1] TRUE
[1] "dimension 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 38 20  4
D32V5, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 62 
        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-A47O         TCGA-B1-A655 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B1-A656         TCGA-B1-A657         TCGA-B9-7268 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5882         TCGA-BQ-5885 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7045 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7050         TCGA-BQ-7051 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-DW-7963 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-F9-A8NY         TCGA-F9-A97G 
"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-GL-A9DC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40Y         TCGA-IA-A83W 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537         TCGA-KV-A74V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-A5E8         TCGA-P4-A5EA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A7SM         TCGA-SX-A7SP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-Y8-A897         TCGA-Y8-A8RZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
                    vv
clus                  M0  M1  MX
  18Q GAIN MUTATED     4   0   3
  18Q GAIN WILD-TYPE  84   8 109
D32V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                4                 84
  M1                0                  8
  MX                3                109
[1] 3 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   7
  18Q GAIN WILD-TYPE  62 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    7
  18Q GAIN WILD-TYPE   62  151
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                 62
  MALE                  7                151
[1] 2 2
[1] FALSE
D32V8, continuous
D32V9, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 33 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-A44B         TCGA-B9-A69E 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-A8LD         TCGA-G7-A8LE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A59T         TCGA-GL-A9DD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-HE-A5NK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A83S         TCGA-IZ-A6M8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-PJ-A5Z9         TCGA-Q2-A5QZ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SR         TCGA-WN-A9G9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RZ 
"18Q GAIN WILD-TYPE" "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     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           0     8
  18Q GAIN WILD-TYPE                        52   139
D32V10, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       0                 52
  WHITE                                           8                139
[1] 4 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   8
  18Q GAIN WILD-TYPE   9 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    8
  18Q GAIN WILD-TYPE    9  167
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                8                167
[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 183   7
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                190 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 0                  7 
$`19P GAIN MUTATED`
TCGA-BQ-5885 TCGA-BQ-5892 TCGA-G7-A8LC TCGA-GL-7966 
         921          364          262          112 

$`19P GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         379          516         1968            2          118           87 
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-B1-7332 TCGA-B1-A47M 
        1357           26           67          595          223          659 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         747          513          108          510           14          200 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379          309 
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          452          167           52         2639          586 
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-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-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
          10            7           36           13          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-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         194          197         1967         1965         5925          393 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
         841           32          378          546           27          341 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         140         2072          408          360         1726         2228 
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          376            4          364          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          845          924          841          616           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        2584         2816          391          540          428         1457 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1443         1005          876          823         1973          578 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 
        1175         1266          805         1469         1331          579 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
         882          224            2          186          219          181 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         399          205          106          104 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               112                  2 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               921               5925 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             313.0              543.5 
[1] "112.0 - 921.0 (313.0)" "2.0 - 5925.0 (543.5)" 
[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     135       16        41       13
D33V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  2                135
  STAGE II                 0                 16
  STAGE III                2                 41
  STAGE IV                 0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  19P GAIN MUTATED     2   0     2
  19P GAIN WILD-TYPE 144  22    49
D33V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                   2                144
  T2                   0                 22
  T3+T4                2                 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
  19P GAIN MUTATED    2  1  0
  19P GAIN WILD-TYPE 37 19  4
D33V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                2                 37
  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     2   0   2
  19P GAIN WILD-TYPE  86   8 110
D33V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                2                 86
  M1                0                  8
  MX                2                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1   3
  19P GAIN WILD-TYPE  62 155
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    3
  19P GAIN WILD-TYPE   62  155
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                1                 62
  MALE                  3                155
[1] 2 2
[1] FALSE
D33V8, continuous
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 1                 55 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8310 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A4ZT         TCGA-A4-A57E 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6796 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LB         TCGA-G7-A8LD 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-IA-A40U         TCGA-IA-A40X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-8537         TCGA-Q2-A5QZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A71S         TCGA-SX-A71U 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-SX-A71V         TCGA-SX-A7SL         TCGA-SX-A7SM 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-SX-A7SN         TCGA-SX-A7SO         TCGA-SX-A7SP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-SX-A7SQ         TCGA-SX-A7SR         TCGA-SX-A7SS 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-SX-A7SU 
"19P GAIN WILD-TYPE" 
D33V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     0
  19P GAIN WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           0     4
  19P GAIN WILD-TYPE                        52   143
D33V10, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       0                 52
  WHITE                                           4                143
[1] 4 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   9 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    4
  19P GAIN WILD-TYPE    9  171
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                4                171
[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 183   7
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                190 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                  7 
$`19Q GAIN MUTATED`
TCGA-BQ-5885 TCGA-BQ-5892 TCGA-G7-A8LC TCGA-GL-7966 
         921          364          262          112 

$`19Q GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         379          516         1968            2          118           87 
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-B1-7332 TCGA-B1-A47M 
        1357           26           67          595          223          659 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         747          513          108          510           14          200 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379          309 
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          452          167           52         2639          586 
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-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-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
          10            7           36           13          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-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         194          197         1967         1965         5925          393 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
         841           32          378          546           27          341 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         140         2072          408          360         1726         2228 
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          376            4          364          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          845          924          841          616           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        2584         2816          391          540          428         1457 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1443         1005          876          823         1973          578 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 
        1175         1266          805         1469         1331          579 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
         882          224            2          186          219          181 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         399          205          106          104 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               112                  2 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               921               5925 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             313.0              543.5 
[1] "112.0 - 921.0 (313.0)" "2.0 - 5925.0 (543.5)" 
[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     135       16        41       13
D34V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  2                135
  STAGE II                 0                 16
  STAGE III                2                 41
  STAGE IV                 0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  19Q GAIN MUTATED     2   0     2
  19Q GAIN WILD-TYPE 144  22    49
D34V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                   2                144
  T2                   0                 22
  T3+T4                2                 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
  19Q GAIN MUTATED    2  1  0
  19Q GAIN WILD-TYPE 37 19  4
D34V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                2                 37
  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     2   0   2
  19Q GAIN WILD-TYPE  86   8 110
D34V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0                2                 86
  M1                0                  8
  MX                2                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1   3
  19Q GAIN WILD-TYPE  62 155
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1    3
  19Q GAIN WILD-TYPE   62  155
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                1                 62
  MALE                  3                155
[1] 2 2
[1] FALSE
D34V8, continuous
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 55 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8310 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A4ZT         TCGA-A4-A57E 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6796 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LB         TCGA-G7-A8LD 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-IA-A40U         TCGA-IA-A40X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-8537         TCGA-Q2-A5QZ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A71S         TCGA-SX-A71U 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-SX-A71V         TCGA-SX-A7SL         TCGA-SX-A7SM 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-SX-A7SN         TCGA-SX-A7SO         TCGA-SX-A7SP 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-SX-A7SQ         TCGA-SX-A7SR         TCGA-SX-A7SS 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-SX-A7SU 
"19Q GAIN WILD-TYPE" 
D34V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     0
  19Q GAIN WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           0     4
  19Q GAIN WILD-TYPE                        52   143
D34V10, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       0                 52
  WHITE                                           4                143
[1] 4 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   9 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0    4
  19Q GAIN WILD-TYPE    9  171
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                4                171
[1] 2 2
[1] FALSE

Clustering(35) Variable = 20P GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    64   2
  20P GAIN WILD-TYPE 123   5
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                66                128 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                  5 
$`20P GAIN MUTATED`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 
         207          554          582           27           49            2 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A5XZ TCGA-A4-A5Y1 
         780          729          597          600            2           87 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
        1636          412           67          223          747          108 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-7268 
        1029          930          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-G7-A8LB TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-A5NF 
        1194          765          197          262          112         2072 
TCGA-HE-A5NI TCGA-IA-A40Y TCGA-IZ-8195 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
         360           62          677          364          885         1043 
TCGA-MH-A562 TCGA-MH-A854 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71V 
         616           11          540          428         1457          876 
TCGA-SX-A7SL TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-WN-AB4C TCGA-Y8-A895 TCGA-Y8-A8S0 
         823         1266         1469          882            2          106 

$`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-A57E TCGA-A4-A5Y0 
          23          436          379          516         1968          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-B1-5398 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         595          659          513          510           14          200 
TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
         307         1049          309         1536          857          803 
TCGA-B9-4116 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         627          460         1338           64          585          207 
TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
         452           52         2639          586          270         1938 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 
        1454         1242          792          921          792          403 
TCGA-BQ-5890 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 
         233         3760         2839         1864         1516          799 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-7834 TCGA-DW-7837 
         612          232          214          218         3950         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         744          419          114           92         1240         2429 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY 
        1856         1670         1040          757           97           36 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 
          13         1575         1479         1059          446          786 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
         194         1967         1965         5925          393          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
          32          378          546           27          341          140 
TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         408         1726         2228          167          511          608 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A74V TCGA-MH-A55Z 
         649          146          376            4          161          845 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
         924          841          369          541          493          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-SX-A71S 
        3035         2653         2584         2816          391         1443 
TCGA-SX-A71U TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SR TCGA-SX-A7SU 
        1005         1973          578         1175          805         1331 
TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
         579          224          186          219          181          399 
TCGA-Y8-A8RZ TCGA-Y8-A8S1 
         205          104 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                  3 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              2948               5925 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             421.0              578.5 
[1] "2.0 - 2948.0 (421.0)" "3.0 - 5925.0 (578.5)"
[1] "hr=" "1.2"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED        47        7        12        4
  20P GAIN WILD-TYPE      90        9        31        9
D35V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                 47                 90
  STAGE II                 7                  9
  STAGE III               12                 31
  STAGE IV                 4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  20P GAIN MUTATED   50 10    14
  20P GAIN WILD-TYPE 96 12    37
D35V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                  50                 96
  T2                  10                 12
  T3+T4               14                 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
  20P GAIN MUTATED   10  6  1
  20P GAIN WILD-TYPE 29 14  3
D35V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               10                 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
  20P GAIN MUTATED   30  2 39
  20P GAIN WILD-TYPE 58  6 73
D35V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               30                 58
  M1                2                  6
  MX               39                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    23  51
  20P GAIN WILD-TYPE  40 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     23   51
  20P GAIN WILD-TYPE   40  107
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               23                 40
  MALE                 51                107
[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     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          14    51
  20P GAIN WILD-TYPE                        38    96
D35V10, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                      14                 38
  WHITE                                          51                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     2  60
  20P GAIN WILD-TYPE   7 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2   60
  20P GAIN WILD-TYPE    7  115
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               60                115
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20Q GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    65   2
  20Q GAIN WILD-TYPE 122   5
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                67                127 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 2                  5 
$`20Q GAIN MUTATED`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 
         207          554          582           27           49            2 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A5XZ TCGA-A4-A5Y1 
         780          729          597          600            2           87 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
        1636          412           67          223          747          108 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4117 TCGA-B9-4617 
        1029          930         1049          379           14           35 
TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 
         671            5          167          771           29          364 
TCGA-BQ-5894 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
          84         2948         1533          116          353          414 
TCGA-DW-7836 TCGA-DW-7841 TCGA-DZ-6132 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-F9-A7VF 
        1093          445         2460          578           10            7 
TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-7966 
         208         1194          765          197          262          112 
TCGA-HE-A5NF TCGA-HE-A5NI TCGA-IA-A40Y TCGA-IZ-8195 TCGA-KV-A6GD TCGA-KV-A6GE 
        2072          360           62          677          364          885 
TCGA-MH-A55W TCGA-MH-A562 TCGA-MH-A854 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        1043          616           11          540          428         1457 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-WN-AB4C TCGA-Y8-A895 
         876          823         1266         1469          882            2 
TCGA-Y8-A8S0 
         106 

$`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-A57E TCGA-A4-A5Y0 
          23          436          379          516         1968          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-B1-5398 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         595          659          513          510           14          200 
TCGA-B3-3926 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
         307          309         1536          857          803          627 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E 
         460         1338           64          585          207          452 
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-5888 TCGA-BQ-5890 
        1242          792          921          792          403          233 
TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        3760         2839         1864         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
         232          214          218         3950         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6134 
         419          114           92         1240         2429         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G 
        1670         1040          757           97           36           13 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
        1575         1479         1059          446          786          194 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
        1967         1965         5925          393          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH 
         378          546           27          341          140          408 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8196 
        1726         2228          167          511          608          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A560 
         146          376            4          161          845          924 
TCGA-MH-A561 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
         841          369          541          493          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-SX-A71S TCGA-SX-A71U 
        2653         2584         2816          391         1443         1005 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SR TCGA-SX-A7SU TCGA-WN-A9G9 
        1973          578         1175          805         1331          579 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
         224          186          219          181          399          205 
TCGA-Y8-A8S1 
         104 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 2                  3 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              2948               5925 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               428                578 
[1] "2.0 - 2948.0 (428.0)" "3.0 - 5925.0 (578.0)"
[1] "hr=" "1.2"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED        47        8        13        4
  20Q GAIN WILD-TYPE      90        8        30        9
D36V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                 47                 90
  STAGE II                 8                  8
  STAGE III               13                 30
  STAGE IV                 4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  20Q GAIN MUTATED   50 11    15
  20Q GAIN WILD-TYPE 96 11    36
D36V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                  50                 96
  T2                  11                 11
  T3+T4               15                 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
  20Q GAIN MUTATED   10  7  1
  20Q GAIN WILD-TYPE 29 13  3
D36V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               10                 29
  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   32  2 39
  20Q GAIN WILD-TYPE 56  6 73
D36V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               32                 56
  M1                2                  6
  MX               39                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    24  52
  20Q GAIN WILD-TYPE  39 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     24   52
  20Q GAIN WILD-TYPE   39  106
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               24                 39
  MALE                 52                106
[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     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                          14    53
  20Q GAIN WILD-TYPE                        38    94
D36V10, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                      14                 38
  WHITE                                          53                 94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     2  61
  20Q GAIN WILD-TYPE   7 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2   61
  20Q GAIN WILD-TYPE    7  114
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               61                114
[1] 2 2
[1] FALSE

Clustering(37) Variable = 21Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    13   0
  21Q GAIN WILD-TYPE 174   7
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                13                181 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 0                  7 
$`21Q GAIN MUTATED`
TCGA-2K-A9WE TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-A6HP TCGA-AT-A5NU TCGA-B1-A47O 
         207          729          709            4           67          513 
TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5892 TCGA-F9-A8NY TCGA-G7-A8LC TCGA-HE-A5NJ 
          14            5          364           36          262         1726 
TCGA-Q2-A5QZ 
         428 

$`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-A57E 
         597          600          436          379          516         1968 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
           2          118           87         1778         1636          412 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-7332 
         923          763         1357           26          595          223 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         659          747          108          510           14          200 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379          309 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 
        1536          857          803          627           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E 
        1338          671           64          585          207          452 
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-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         403          233           29           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-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
           7           13          208         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
        1059          765          446          786          194          197 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
        1967         1965         5925          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
          32          378          546           27          341          140 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         2228          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          376 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
           4          364          885          161         1043          845 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
         924          841          616           11          369          541 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         493          148         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         391          540         1457         1443         1005          876 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR 
         823         1973          578         1175         1266          805 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
        1469         1331          579          882          224            2 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
         186          219          181          399          205          106 
TCGA-Y8-A8S1 
         104 

  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 
               262                578 
[1] "4.0 - 1726.0 (262.0)" "2.0 - 5925.0 (578.0)"
[1] "hr="     "2.6e+07"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED         9        1         2        1
  21Q GAIN WILD-TYPE     128       15        41       12
D37V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  9                128
  STAGE II                 1                 15
  STAGE III                2                 41
  STAGE IV                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  21Q GAIN MUTATED    10   2     3
  21Q GAIN WILD-TYPE 136  20    48
D37V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                  10                136
  T2                   2                 20
  T3+T4                3                 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
  21Q GAIN MUTATED    2  2  0
  21Q GAIN WILD-TYPE 37 18  4
D37V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                2                 37
  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     3   1  10
  21Q GAIN WILD-TYPE  85   7 102
D37V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                3                 85
  M1                1                  7
  MX               10                102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     5  10
  21Q GAIN WILD-TYPE  58 148
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      5   10
  21Q GAIN WILD-TYPE   58  148
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                5                 58
  MALE                 10                148
[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                 33 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-A44B         TCGA-B9-A69E 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-A8LB         TCGA-G7-A8LD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-7773         TCGA-GL-A59T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-HE-A5NK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A83S         TCGA-IZ-A6M8 
"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-A7SR         TCGA-SX-A7SS         TCGA-WN-A9G9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  1     1
  21Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           3     9
  21Q GAIN WILD-TYPE                        49   138
D37V10, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       3                 49
  WHITE                                           9                138
[1] 4 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  13
  21Q GAIN WILD-TYPE   8 162
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   13
  21Q GAIN WILD-TYPE    8  162
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               13                162
[1] 2 2
[1] FALSE

Clustering(38) Variable = 22Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED     2   0
  22Q GAIN WILD-TYPE 185   7
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                192 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 0                  7 
$`22Q GAIN MUTATED`
TCGA-BQ-5892 TCGA-G7-A8LB 
         364          197 

$`22Q GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         379          516         1968            2          118           87 
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-B1-7332 TCGA-B1-A47M 
        1357           26           67          595          223          659 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         747          513          108          510           14          200 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379          309 
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          452          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-F9-A97G TCGA-G7-6789 
          97           10            7           36           13          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-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
         786          194          262         1967         1965         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          378          546 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          27          341          140         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
        1726         2228          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          376            4          364 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          845          924          841 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
         616           11          369          541          493          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3035         2653         2584         2816          391          540 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
         428         1457         1443         1005          876          823 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
        1973          578         1175         1266          805         1469 
TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
        1331          579          882          224            2          186 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         219          181          399          205          106          104 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               197                  2 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               364               5925 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             280.5              543.5 
[1] "197.0 - 364.0 (280.5)" "2.0 - 5925.0 (543.5)" 
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q GAIN MUTATED         2        0         0        1
  22Q GAIN WILD-TYPE     135       16        43       12
D38V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  2                135
  STAGE II                 0                 16
  STAGE III                0                 43
  STAGE IV                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  22Q GAIN MUTATED     2   1     0
  22Q GAIN WILD-TYPE 144  21    51
D38V4, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                   2                144
  T2                   1                 21
  T3+T4                0                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  22Q GAIN MUTATED    1  0  0
  22Q GAIN WILD-TYPE 38 20  4
D38V5, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 62 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y1         TCGA-AL-3466 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-A47O         TCGA-B1-A655 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B1-A656         TCGA-B1-A657         TCGA-B9-7268 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5882         TCGA-BQ-5885 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5893 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7045         TCGA-BQ-7048 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7056 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-DW-7963         TCGA-DZ-6131 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F9-A8NY         TCGA-F9-A97G         TCGA-G7-6789 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-7501 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-GL-6846         TCGA-GL-7966 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GL-A59R         TCGA-GL-A9DC         TCGA-IA-A40U 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IA-A83W         TCGA-J7-6720 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-J7-8537         TCGA-KV-A74V         TCGA-P4-A5E6 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-P4-A5E8         TCGA-P4-A5EA         TCGA-SX-A71R 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SP         TCGA-SX-A7SS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-Y8-A897         TCGA-Y8-A8RZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
                    vv
clus                  M0  M1  MX
  22Q GAIN MUTATED     1   0   2
  22Q GAIN WILD-TYPE  87   8 110
D38V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0                1                 87
  M1                0                  8
  MX                2                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0   3
  22Q GAIN WILD-TYPE  63 155
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    3
  22Q GAIN WILD-TYPE   63  155
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                0                 63
  MALE                  3                155
[1] 2 2
[1] FALSE
D38V8, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 55 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8310 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A4ZT         TCGA-A4-A57E 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6796 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LC         TCGA-G7-A8LD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-IA-A40U         TCGA-IA-A40X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-8537         TCGA-Q2-A5QZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A71S         TCGA-SX-A71U 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A71V         TCGA-SX-A7SL         TCGA-SX-A7SM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A7SN         TCGA-SX-A7SO         TCGA-SX-A7SP 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A7SQ         TCGA-SX-A7SR         TCGA-SX-A7SS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A7SU 
"22Q GAIN WILD-TYPE" 
D38V9, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 34 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-A44B         TCGA-B9-A69E 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-A8LD         TCGA-G7-A8LE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A59T         TCGA-GL-A9DD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-HE-A5NK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A83S         TCGA-IZ-A6M8 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-PJ-A5Z9         TCGA-Q2-A5QZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SR         TCGA-SX-A7SS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-Y8-A894         TCGA-Y8-A896 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ 
"22Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0     0
  22Q GAIN WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           0     3
  22Q GAIN WILD-TYPE                        52   144
D38V10, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       0                 52
  WHITE                                           3                144
[1] 4 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
  22Q GAIN MUTATED     1   2
  22Q GAIN WILD-TYPE   8 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1    2
  22Q GAIN WILD-TYPE    8  173
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO                2                173
[1] 2 2
[1] FALSE

Clustering(39) Variable = XQ GAIN MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    60   1
  XQ GAIN WILD-TYPE 127   6
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               61               133 
  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-B1-A657 TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4113 
         659          747          200          930          309         1536 
TCGA-B9-4114 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-A44B 
         857          627           14           35         1338           64 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-7046 
           5          167         1454          771           29         2948 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7836 TCGA-DW-7963 TCGA-F9-A7VF TCGA-F9-A8NY 
         214          116         1093         1240            7           36 
TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-GL-6846 TCGA-GL-A59T 
        1575         1194          194          197         5925          546 
TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-KV-A6GD TCGA-KV-A6GE 
        2072          360         1726          167          364          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-PJ-A5Z9 
         161         1043          845         2653         2584          540 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
        1005          876          578         1266          805         1469 
TCGA-Y8-A895 
           2 

$`XQ GAIN WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          780 
TCGA-A4-8518 TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3467 TCGA-AL-3472 
         600         1968          118           87         1778          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47O 
         763         1357           26          595          223          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 
         108          510           14         1029          307         1049 
TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 
         379          803          460          671          585          207 
TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
         452           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-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
         364           84         3760         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 
        1516          799          612          232          218          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
         414         3950         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
         445           92         2429         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G 
        1040          578          757           97           10           13 
TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
         208         1479         1059          765          446          786 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
         262         1967         1965          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH 
          32          378           27          341          140          408 
TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        2228          511          608           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         146          376            4          924          841          616 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
          11          369          541          493          148         3035 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A7SL 
        2816          391          428         1457         1443          823 
TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
        1973         1175         1331          579          882          224 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
         186          219          181          399          205          106 
TCGA-Y8-A8S1 
         104 

  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 
              597               510 
[1] "2.0 - 5925.0 (597.0)" "2.0 - 3950.0 (510.0)"
[1] "hr=" "2.7"
D39V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED        51        3         6        4
  XQ GAIN WILD-TYPE      86       13        37        9
D39V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                51                86
  STAGE II                3                13
  STAGE III               6                37
  STAGE IV                4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  XQ GAIN MUTATED   53  8     9
  XQ GAIN WILD-TYPE 93 14    42
D39V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1                 53                93
  T2                  8                14
  T3+T4               9                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
  XQ GAIN MUTATED    9  3  0
  XQ GAIN WILD-TYPE 30 17  4
D39V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0               9                30
  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   26  2 35
  XQ GAIN WILD-TYPE 62  6 77
D39V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0              26                62
  M1               2                 6
  MX              35                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"
D39V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    14  56
  XQ GAIN WILD-TYPE  49 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     14   56
  XQ GAIN WILD-TYPE   49  102
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              14                49
  MALE                56               102
[1] 2 2
[1] FALSE
D39V8, continuous
D39V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  2     1
  XQ GAIN WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                          16    44
  XQ GAIN WILD-TYPE                        36   103
D39V10, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                     16                36
  WHITE                                         44               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"
D39V11, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     2  57
  XQ GAIN WILD-TYPE   7 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2   57
  XQ GAIN WILD-TYPE    7  118
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              57               118
[1] 2 2
[1] FALSE

Clustering(40) Variable = 1P LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    18   1
  1P LOSS WILD-TYPE 169   6
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               19               175 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                 6 
$`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-G7-6797 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-8500 TCGA-HE-A5NK TCGA-PJ-A5Z8 
         765          786          262          841         2228          391 
TCGA-Q2-A5QZ 
         428 

$`1P LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207           21          493          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
          49            2          780          729          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         1968 
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-A47O TCGA-B1-A654 TCGA-B1-A655 
         595          659          747          513          108          510 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
          14          200         1029          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
         309         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-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 
           5          452          167           52          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-7046 
         771          403          233           29          364         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7059 
        2839         1864         1533         1516          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-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
        1040          578          757            7           36           13 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 
         208         1575         1479         1194         1059          446 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         194          197         1967         1965         5925          393 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
         112           32          378          546           27          341 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
         140         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 
         376            4          364          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         541          493          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
        2816          540         1457         1443         1005          876 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR 
         823         1973          578         1175         1266          805 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
        1469         1331          579          882          224            2 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
         186          219          181          399          205          106 
TCGA-Y8-A8S1 
         104 

  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 
              391               546 
[1] "3.0 - 3760.0 (391.0)" "2.0 - 5925.0 (546.0)"
[1] "hr=" "1.2"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED         9        2         7        1
  1P LOSS WILD-TYPE     128       14        36       12
D40V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 9               128
  STAGE II                2                14
  STAGE III               7                36
  STAGE IV                1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  1P LOSS MUTATED    11   2     8
  1P LOSS WILD-TYPE 135  20    43
D40V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1                 11               135
  T2                  2                20
  T3+T4               8                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
  1P LOSS MUTATED    2  2  0
  1P LOSS WILD-TYPE 37 18  4
D40V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0               2                37
  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
  1P LOSS MUTATED    10   1   9
  1P LOSS WILD-TYPE  78   7 103
D40V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0              10                78
  M1               1                 7
  MX               9               103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     8  13
  1P LOSS WILD-TYPE  55 145
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      8   13
  1P LOSS WILD-TYPE   55  145
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               8                55
  MALE                13               145
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, continuous
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                33 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-B1-A654 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A69E        TCGA-F9-A97G        TCGA-G7-A8LB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A59T 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-IA-A40U 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IA-A83S        TCGA-IZ-A6M8        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-A7SR 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-WN-A9G9        TCGA-Y8-A894        TCGA-Y8-A896 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-Y8-A8RZ 
"1P LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     1
  1P LOSS WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           6    11
  1P LOSS WILD-TYPE                        46   136
D40V10, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      6                46
  WHITE                                         11               136
[1] 4 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
  1P LOSS MUTATED     1  14
  1P LOSS WILD-TYPE   8 161
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1   14
  1P LOSS WILD-TYPE    8  161
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              14               161
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1Q LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    15   0
  1Q LOSS WILD-TYPE 172   7
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               15               179 
  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-G7-A8LC TCGA-GL-8500 
          84           10          765          786          262          841 
TCGA-HE-A5NK TCGA-PJ-A5Z8 TCGA-Q2-A5QZ 
        2228          391          428 

$`1Q LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207           21          493          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
        1968            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-A47O TCGA-B1-A654 
          67          595          659          747          513          108 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
          14          200         1029          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
         309         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-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
           5          452          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-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
          97            7           36           13          208         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB 
        1479         1194         1059          446          194          197 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM 
        1967         1965         5925          393          112           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
         378          546           27          341          140         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          376            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         364          885          161         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
         841          616           11          369          541          493 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 
         148         3035         2653         2584         2816          540 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1457         1443         1005          876          823         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
         578         1175         1266          805         1469         1331 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
         579          882          224            2          186          219 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         181          399          205          106          104 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3                 2 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             2228              5925 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              391               578 
[1] "3.0 - 2228.0 (391.0)" "2.0 - 5925.0 (578.0)"
[1] "hr="     "7.3e+07"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED         8        2         3        1
  1Q LOSS WILD-TYPE     129       14        40       12
D41V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 8               129
  STAGE II                2                14
  STAGE III               3                40
  STAGE IV                1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  1Q LOSS MUTATED    10   2     4
  1Q LOSS WILD-TYPE 136  20    47
D41V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1                 10               136
  T2                  2                20
  T3+T4               4                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 37 18  4
D41V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0               2                37
  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     7   1   7
  1Q LOSS WILD-TYPE  81   7 105
D41V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               7                81
  M1               1                 7
  MX               7               105
[1] 3 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
  1Q LOSS MUTATED     7   9
  1Q LOSS WILD-TYPE  56 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      7    9
  1Q LOSS WILD-TYPE   56  149
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               7                56
  MALE                 9               149
[1] 2 2
[1] FALSE
D41V8, continuous
D41V9, continuous
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2                33 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-B1-A654 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A69E        TCGA-F9-A97G        TCGA-G7-A8LB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A59T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-IA-A40U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IA-A83S        TCGA-IZ-A6M8        TCGA-MH-A854        TCGA-MH-A856 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9        TCGA-SX-A71S 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-WN-A9G9        TCGA-Y8-A894        TCGA-Y8-A896 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-Y8-A8RZ 
"1Q LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     1
  1Q LOSS WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           4     9
  1Q LOSS WILD-TYPE                        48   138
D41V10, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      4                48
  WHITE                                          9               138
[1] 4 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
  1Q LOSS MUTATED     1  14
  1Q LOSS WILD-TYPE   8 161
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   14
  1Q LOSS WILD-TYPE    8  161
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              14               161
[1] 2 2
[1] FALSE

Clustering(42) Variable = 3P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    13   3
  3P LOSS WILD-TYPE 174   4
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               16               178 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3                 4 
$`3P LOSS MUTATED`
TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3473 TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5877 
        1968           87          763           64          452          270 
TCGA-BQ-5892 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-7966 TCGA-IA-A40Y 
         364         2429          208          262          112           62 
TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-WN-A9G9 TCGA-Y8-A8RZ 
           4          428          579          205 

$`3P LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
         379          516            2          118            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
        1636          412          923         1357           26           67 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
         595          223          659          747          513          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         510           14          200         1029          307          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379          309         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-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-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         586         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-6132 
         419          114          445           92         1240         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-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
          10            7           36           13         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          194 
TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
         197         1967         1965         5925          393          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
          32          378          546           27          341          140 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
        2072          408          360         1726         2228          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         511          608          677          649          146          376 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         364          885          161         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
         841          616           11          369          541          493 
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 
         540         1457         1443         1005          876          823 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
        1973          578         1175         1266          805         1469 
TCGA-SX-A7SU TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
        1331          882          224            2          186          219 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         181          399          106          104 

  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 
              266               578 
[1] "4.0 - 2429.0 (266.0)" "2.0 - 5925.0 (578.0)"
[1] "hr=" "9.1"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED         4        1         9        3
  3P LOSS WILD-TYPE     133       15        34       10
D42V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 4               133
  STAGE II                1                15
  STAGE III               9                34
  STAGE IV                3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  3P LOSS MUTATED     5   2    10
  3P LOSS WILD-TYPE 141  20    41
D42V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1                  5               141
  T2                  2                20
  T3+T4              10                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
  3P LOSS MUTATED    6  5  1
  3P LOSS WILD-TYPE 33 15  3
D42V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0               6                33
  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   9
  3P LOSS WILD-TYPE  84   6 103
D42V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0               4                84
  M1               2                 6
  MX               9               103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     5  12
  3P LOSS WILD-TYPE  58 146
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5   12
  3P LOSS WILD-TYPE   58  146
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               5                58
  MALE                12               146
[1] 2 2
[1] FALSE
D42V8, continuous
D42V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0     1
  3P LOSS WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                           3    12
  3P LOSS WILD-TYPE                        49   135
D42V10, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      3                49
  WHITE                                         12               135
[1] 4 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
  3P LOSS MUTATED     0  14
  3P LOSS WILD-TYPE   9 161
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0   14
  3P LOSS WILD-TYPE    9  161
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              14               161
[1] 2 2
[1] FALSE

Clustering(43) Variable = 3Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     2   2
  3Q LOSS WILD-TYPE 185   5
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               190 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                 5 
$`3Q LOSS MUTATED`
TCGA-BQ-5877 TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-7966 
         270          208          262          112 

$`3Q LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         379          516         1968            2          118           87 
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-B1-7332 TCGA-B1-A47M 
        1357           26           67          595          223          659 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         747          513          108          510           14          200 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379          309 
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          452          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-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-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
          97           10            7           36           13         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-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         194          197         1967         1965         5925          393 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
         841           32          378          546           27          341 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         140         2072          408          360         1726         2228 
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          376            4          364          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          845          924          841          616           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        2584         2816          391          540          428         1457 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1443         1005          876          823         1973          578 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 
        1175         1266          805         1469         1331          579 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
         882          224            2          186          219          181 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         399          205          106          104 

  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 
              235               550 
[1] "112.0 - 270.0 (235.0)" "2.0 - 5925.0 (550.0)" 
[1] "hr=" "55" 
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED         1        0         2        2
  3Q LOSS WILD-TYPE     136       16        41       11
D43V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 1               136
  STAGE II                0                16
  STAGE III               2                41
  STAGE IV                2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  3Q LOSS MUTATED     1   0     4
  3Q LOSS WILD-TYPE 145  22    47
D43V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1                  1               145
  T2                  0                22
  T3+T4               4                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
  3Q LOSS MUTATED    1  2  1
  3Q LOSS WILD-TYPE 38 18  3
D43V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0               1                38
  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   3
  3Q LOSS WILD-TYPE  87   7 109
D43V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               1                87
  M1               1                 7
  MX               3               109
[1] 3 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
  3Q LOSS MUTATED     2   3
  3Q LOSS WILD-TYPE  61 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    3
  3Q LOSS WILD-TYPE   61  155
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               2                61
  MALE                 3               155
[1] 2 2
[1] FALSE
D43V8, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                55 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8310        TCGA-A4-8311 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-8312        TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A4ZT 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-7502        TCGA-G7-A4TM        TCGA-G7-A8LB        TCGA-G7-A8LD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-A8LE        TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-J7-8537        TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SX-A7SN        TCGA-SX-A7SO        TCGA-SX-A7SP        TCGA-SX-A7SQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-SX-A7SU 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D43V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     0
  3Q LOSS WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           1     3
  3Q LOSS WILD-TYPE                        51   144
D43V10, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                51
  WHITE                                          3               144
[1] 4 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
  3Q LOSS MUTATED     0   3
  3Q LOSS WILD-TYPE   9 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    3
  3Q LOSS WILD-TYPE    9  172
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               3               172
[1] 2 2
[1] FALSE

Clustering(44) Variable = 4P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    13   2
  4P LOSS WILD-TYPE 174   5
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               15               179 
  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-HE-A5NK 
          97           10          446         1967          112         2228 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ 
          62            4          428 

$`4P LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207          554          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
         516         1968            2          118           87            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
          67          595          659          747          513          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
         510           14          200         1029          930         1049 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
         379          309         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          452          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-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        1240         2460         1856         1670         1040          578 
TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
         757            7           36           13          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          194 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
         197          262         1965         5925          393          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
          32          378          546           27          341          140 
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          376          364 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          845          924          841 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
         616           11          369          541          493          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3035         2653         2584         2816          391          540 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1457         1443         1005          876          823         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
         578         1175         1266          805         1469         1331 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
         579          882          224            2          186          219 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         181          399          205          106          104 

  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 
              112               578 
[1] "4.0 - 2429.0 (112.0)" "2.0 - 5925.0 (578.0)"
[1] "hr=" "4.4"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P LOSS MUTATED         3        1        14        1
  4P LOSS WILD-TYPE     134       15        29       12
D44V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 3               134
  STAGE II                1                15
  STAGE III              14                29
  STAGE IV                1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  4P LOSS MUTATED     4   2    14
  4P LOSS WILD-TYPE 142  20    37
D44V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1                  4               142
  T2                  2                20
  T3+T4              14                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
  4P LOSS MUTATED    2  9  0
  4P LOSS WILD-TYPE 37 11  4
D44V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0               2                37
  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     8   1  11
  4P LOSS WILD-TYPE  80   7 101
D44V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0               8                80
  M1               1                 7
  MX              11               101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    14   6
  4P LOSS WILD-TYPE  49 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     14    6
  4P LOSS WILD-TYPE   49  152
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              14                49
  MALE                 6               152
[1] 2 2
[1] FALSE
D44V8, continuous
D44V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     2
  4P LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                           4    10
  4P LOSS WILD-TYPE                        48   137
D44V10, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 3
  BLACK OR AFRICAN AMERICAN                      4                48
  WHITE                                         10               137
[1] 4 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
  4P LOSS MUTATED     1  13
  4P LOSS WILD-TYPE   8 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   13
  4P LOSS WILD-TYPE    8  162
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              13               162
[1] 2 2
[1] FALSE

Clustering(45) Variable = 4Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    15   2
  4Q LOSS WILD-TYPE 172   5
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               17               177 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                 5 
$`4Q LOSS MUTATED`
TCGA-A4-7287 TCGA-A4-A57E TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5876 
          21         1968           26          223          307          586 
TCGA-BQ-5894 TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-7501 TCGA-G7-A8LD 
          84         2429           97           10          446         1967 
TCGA-GL-7966 TCGA-HE-A5NK TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ 
         112         2228           62            4          428 

$`4Q LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207          554          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-A47O TCGA-B1-A654 TCGA-B1-A655 
         595          659          747          513          108          510 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
          14          200         1029          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
         309         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          452          167           52         2639 
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-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-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
          36           13          208         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
        1059          765          786          194          197          262 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        1965         5925          393          841           32          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
         546           27          341          140         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          376          364          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          845          924          841          616           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
        2584         2816          391          540         1457         1443 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1005          876          823         1973          578         1175 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C 
        1266          805         1469         1331          579          882 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
         224            2          186          219          181          399 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         205          106          104 

  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 
              223               578 
[1] "4.0 - 2429.0 (223.0)" "2.0 - 5925.0 (578.0)"
[1] "hr=" "3.4"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED         4        1        13        2
  4Q LOSS WILD-TYPE     133       15        30       11
D45V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 4               133
  STAGE II                1                15
  STAGE III              13                30
  STAGE IV                2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  4Q LOSS MUTATED     5   3    13
  4Q LOSS WILD-TYPE 141  19    38
D45V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1                  5               141
  T2                  3                19
  T3+T4              13                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
  4Q LOSS MUTATED    3  8  0
  4Q LOSS WILD-TYPE 36 12  4
D45V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0               3                36
  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     8   2  11
  4Q LOSS WILD-TYPE  80   6 101
D45V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0               8                80
  M1               2                 6
  MX              11               101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    13   8
  4Q LOSS WILD-TYPE  50 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     13    8
  4Q LOSS WILD-TYPE   50  150
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              13                50
  MALE                 8               150
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0     2
  4Q LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                           4    11
  4Q LOSS WILD-TYPE                        48   136
D45V10, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 3
  BLACK OR AFRICAN AMERICAN                      4                48
  WHITE                                         11               136
[1] 4 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
  4Q LOSS MUTATED     1  14
  4Q LOSS WILD-TYPE   8 161
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1   14
  4Q LOSS WILD-TYPE    8  161
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              14               161
[1] 2 2
[1] FALSE

Clustering(46) Variable = 5P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     4   1
  5P LOSS WILD-TYPE 183   6
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                5               189 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                 6 
$`5P LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7997 TCGA-BQ-5894 TCGA-F9-A4JJ 
         554           21            2           84           97 

$`5P LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
          49          140          780          729          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         1968 
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-A47O TCGA-B1-A654 
         595          223          659          747          513          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         510           14          200         1029          307          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379          309         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          452          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-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-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-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          13          208         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
         765          446          786          194          197          262 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
        1967         1965         5925          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
          32          378          546           27          341          140 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
        2072          408          360         1726         2228          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 
         376            4          364          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         541          493          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
        2816          391          540          428         1457         1443 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1005          876          823         1973          578         1175 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C 
        1266          805         1469         1331          579          882 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
         224            2          186          219          181          399 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         205          106          104 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                 2 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              554              5925 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               84               546 
[1] "2.0 - 554.0 (84.0)"   "2.0 - 5925.0 (546.0)"
[1] "hr=" "34" 
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         2        0         3        2
  5P LOSS WILD-TYPE     135       16        40       11
D46V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 2               135
  STAGE II                0                16
  STAGE III               3                40
  STAGE IV                2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  5P LOSS MUTATED     2   0     6
  5P LOSS WILD-TYPE 144  22    45
D46V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1                  2               144
  T2                  0                22
  T3+T4               6                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
  5P LOSS MUTATED    0  3  1
  5P LOSS WILD-TYPE 39 17  3
D46V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0               0                39
  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     2   1   4
  5P LOSS WILD-TYPE  86   7 108
D46V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               2                86
  M1               1                 7
  MX               4               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     5   3
  5P LOSS WILD-TYPE  58 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5    3
  5P LOSS WILD-TYPE   58  155
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               5                58
  MALE                 3               155
[1] 2 2
[1] FALSE
D46V8, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                54 
       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-A8LB        TCGA-G7-A8LC        TCGA-G7-A8LD        TCGA-G7-A8LE 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-J7-8537 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S        TCGA-SX-A71U 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SN 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-SX-A7SO        TCGA-SX-A7SP        TCGA-SX-A7SQ        TCGA-SX-A7SR 
"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" 
D46V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     0
  5P LOSS WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           1     6
  5P LOSS WILD-TYPE                        51   141
D46V10, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                51
  WHITE                                          6               141
[1] 4 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
  5P LOSS MUTATED     1   5
  5P LOSS WILD-TYPE   8 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1    5
  5P LOSS WILD-TYPE    8  170
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO               5               170
[1] 2 2
[1] FALSE

Clustering(47) Variable = 5Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED     5   1
  5Q LOSS WILD-TYPE 182   6
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6               188 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                 6 
$`5Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7997 TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-GL-7966 
         554           21            2           84           97          112 

$`5Q LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
          49          140          780          729          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         1968 
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-A47O TCGA-B1-A654 
         595          223          659          747          513          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         510           14          200         1029          307          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379          309         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          452          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-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-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-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          13          208         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
         765          446          786          194          197          262 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
        1967         1965         5925          393          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
         378          546           27          341          140         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
         408          360         1726         2228          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          376 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
           4          364          885          161         1043          845 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
         924          841          616           11          369          541 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         493          148         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
         391          540          428         1457         1443         1005 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         876          823         1973          578         1175         1266 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
         805         1469         1331          579          882          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
           2          186          219          181          399          205 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         106          104 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                 2 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              554              5925 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             90.5             562.0 
[1] "2.0 - 554.0 (90.5)"   "2.0 - 5925.0 (562.0)"
[1] "hr=" "27" 
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         2        0         4        1
  5Q LOSS WILD-TYPE     135       16        39       12
D47V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 2               135
  STAGE II                0                16
  STAGE III               4                39
  STAGE IV                1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  5Q LOSS MUTATED     2   0     6
  5Q LOSS WILD-TYPE 144  22    45
D47V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1                  2               144
  T2                  0                22
  T3+T4               6                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
  5Q LOSS MUTATED    0  4  0
  5Q LOSS WILD-TYPE 39 16  4
D47V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0               0                39
  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     2   1   4
  5Q LOSS WILD-TYPE  86   7 108
D47V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               2                86
  M1               1                 7
  MX               4               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     5   3
  5Q LOSS WILD-TYPE  58 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5    3
  5Q LOSS WILD-TYPE   58  155
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               5                58
  MALE                 3               155
[1] 2 2
[1] FALSE
D47V8, continuous
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                55 
       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-A8LB        TCGA-G7-A8LC        TCGA-G7-A8LD 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-A8LE        TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-J7-8537        TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-SX-A7SN        TCGA-SX-A7SO        TCGA-SX-A7SP        TCGA-SX-A7SQ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-SX-A7SU 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
D47V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  0     0
  5Q LOSS WILD-TYPE                                2     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                           1     6
  5Q LOSS WILD-TYPE                        51   141
D47V10, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                51
  WHITE                                          6               141
[1] 4 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
  5Q LOSS MUTATED     1   5
  5Q LOSS WILD-TYPE   8 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1    5
  5Q LOSS WILD-TYPE    8  170
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO               5               170
[1] 2 2
[1] FALSE

Clustering(48) Variable = 6P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    11   1
  6P LOSS WILD-TYPE 176   6
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               12               182 
  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-G7-A8LC TCGA-GL-7966 TCGA-SX-A7SL TCGA-Y8-A896 
         765          786          262          112          823          186 

$`6P LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207           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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
         516         1968            2          118           87            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          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-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         513          108          510           14          200         1029 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         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          452 
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-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-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY 
        1670         1040          757           97            7           36 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 
          13         1575         1479         1194         1059          446 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         194          197         1967         1965         5925          393 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
         841           32          378          546           27          341 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         140         2072          408          360         1726         2228 
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          376            4          364          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          845          924          841          616           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        2584         2816          391          540          428         1457 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1443         1005          876         1973          578         1175 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C 
        1266          805         1469         1331          579          882 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
         224            2          219          181          399          205 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         106          104 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               10                 2 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              823              5925 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            430.5             540.5 
[1] "10.0 - 823.0 (430.5)" "2.0 - 5925.0 (540.5)"
[1] "hr=" "5"  
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED         6        0         7        2
  6P LOSS WILD-TYPE     131       16        36       11
D48V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 6               131
  STAGE II                0                16
  STAGE III               7                36
  STAGE IV                2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  6P LOSS MUTATED     7   1     8
  6P LOSS WILD-TYPE 139  21    43
D48V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1                  7               139
  T2                  1                21
  T3+T4               8                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 LOSS MUTATED    2  2  2
  6P LOSS WILD-TYPE 37 18  2
D48V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0               2                37
  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   7
  6P LOSS WILD-TYPE  80   8 105
D48V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               8                80
  M1               0                 8
  MX               7               105
[1] 3 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
  6P LOSS MUTATED     7   9
  6P LOSS WILD-TYPE  56 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      7    9
  6P LOSS WILD-TYPE   56  149
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               7                56
  MALE                 9               149
[1] 2 2
[1] FALSE
D48V8, continuous
D48V9, continuous
[1] "Remove cluster labels:" "6P LOSS MUTATED"       
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2                33 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-B1-A654 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A69E        TCGA-F9-A97G        TCGA-G7-A8LB 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A59T 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A83S        TCGA-IZ-A6M8        TCGA-MH-A854 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SM 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-WN-A9G9        TCGA-Y8-A894 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-Y8-A8RZ 
"6P LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     1
  6P LOSS WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           0    12
  6P LOSS WILD-TYPE                        52   135
D48V10, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      0                52
  WHITE                                         12               135
[1] 4 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
  6P LOSS MUTATED     0  12
  6P LOSS WILD-TYPE   9 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   12
  6P LOSS WILD-TYPE    9  163
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              12               163
[1] 2 2
[1] FALSE

Clustering(49) Variable = 6Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    15   1
  6Q LOSS WILD-TYPE 172   6
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               16               178 
  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-G7-A8LC TCGA-GL-7966 
         578           10          208          786          262          112 
TCGA-J7-8537 TCGA-P4-A5EB TCGA-SX-A7SL TCGA-Y8-A896 
           4         2584          823          186 

$`6Q LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207           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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
         516         1968            2          118           87            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          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-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         513          108          510           14          200         1029 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         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          452          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-5890 TCGA-BQ-5891 
         792          921          792          771          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-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1533         1516          799          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-5903 
        2429         2460         1856         1670         1040          757 
TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
          97            7           36           13         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB 
        1194         1059          765          446          194          197 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
        1967         1965         5925          393          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
         378          546           27          341          140         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
         408          360         1726         2228          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          376 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         364          885          161         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
         841          616           11          369          541          493 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
         148         3035         2653         2816          391          540 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM 
         428         1457         1443         1005          876         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
         578         1175         1266          805         1469         1331 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 
         579          882          224            2          219          181 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         399          205          106          104 

  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 
            355.0             543.5 
[1] "4.0 - 2639.0 (355.0)" "2.0 - 5925.0 (543.5)"
[1] "hr=" "1.7"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED         8        0         8        2
  6Q LOSS WILD-TYPE     129       16        35       11
D49V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 8               129
  STAGE II                0                16
  STAGE III               8                35
  STAGE IV                2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  6Q LOSS MUTATED     8   0    11
  6Q LOSS WILD-TYPE 138  22    40
D49V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1                  8               138
  T2                  0                22
  T3+T4              11                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
  6Q LOSS MUTATED    3  2  2
  6Q LOSS WILD-TYPE 36 18  2
D49V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0               3                36
  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   7
  6Q LOSS WILD-TYPE  78   8 105
D49V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              10                78
  M1               0                 8
  MX               7               105
[1] 3 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
  6Q LOSS MUTATED    10   9
  6Q LOSS WILD-TYPE  53 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     10    9
  6Q LOSS WILD-TYPE   53  149
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              10                53
  MALE                 9               149
[1] 2 2
[1] FALSE
D49V8, continuous
D49V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0     2
  6Q LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           1    13
  6Q LOSS WILD-TYPE                        51   134
D49V10, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 3
  BLACK OR AFRICAN AMERICAN                      1                51
  WHITE                                         13               134
[1] 4 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
  6Q LOSS MUTATED     0  13
  6Q LOSS WILD-TYPE   9 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0   13
  6Q LOSS WILD-TYPE    9  162
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              13               162
[1] 2 2
[1] FALSE

Clustering(50) Variable = 8P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED     7   2
  8P LOSS WILD-TYPE 180   5
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                9               185 
  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-A8LC TCGA-G7-A8LD TCGA-SX-A7SO 
         262         1967         1175 

$`8P LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
         379          516         1968            2          118            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
          26           67          595          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 
         108          510           14          200         1029          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379          309         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          452          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-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-5561 TCGA-DW-7834 
         232          214          218          116          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-A7VF TCGA-F9-A97G 
        1040          578          757           97            7           13 
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-A8LB TCGA-G7-A8LE TCGA-GL-6846 
         446          786          194          197         1965         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          378          546 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          27          341          140         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
        1726         2228          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          376            4          364 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          845          924          841 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
         616           11          369          541          493          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3035         2653         2584         2816          391          540 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
         428         1457         1443         1005          876          823 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
        1973          578         1266          805         1469         1331 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
         579          882          224            2          186          219 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         181          399          205          106          104 

  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 
              262               554 
[1] "10.0 - 1967.0 (262.0)" "2.0 - 5925.0 (554.0)" 
[1] "hr=" "12" 
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED         5        1         2        3
  8P LOSS WILD-TYPE     132       15        41       10
D50V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 5               132
  STAGE II                1                15
  STAGE III               2                41
  STAGE IV                3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  8P LOSS MUTATED     6   1     4
  8P LOSS WILD-TYPE 140  21    47
D50V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1                  6               140
  T2                  1                21
  T3+T4               4                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
  8P LOSS MUTATED    0  5  0
  8P LOSS WILD-TYPE 39 15  4
D50V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0               0                39
  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   4
  8P LOSS WILD-TYPE  84   5 108
D50V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0               4                84
  M1               3                 5
  MX               4               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     5   6
  8P LOSS WILD-TYPE  58 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5    6
  8P LOSS WILD-TYPE   58  152
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               5                58
  MALE                 6               152
[1] 2 2
[1] FALSE
D50V8, continuous
D50V9, continuous
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                34 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-B1-A654 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A69E        TCGA-F9-A97G        TCGA-G7-A8LB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A59T        TCGA-GL-A9DD 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK        TCGA-IA-A40U 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IA-A83S        TCGA-IZ-A6M8        TCGA-MH-A854        TCGA-MH-A856 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9        TCGA-Q2-A5QZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-WN-A9G9        TCGA-Y8-A894 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A8RZ 
"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     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                           1     8
  8P LOSS WILD-TYPE                        51   139
D50V10, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 3
  BLACK OR AFRICAN AMERICAN                      1                51
  WHITE                                          8               139
[1] 4 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
  8P LOSS MUTATED     0  11
  8P LOSS WILD-TYPE   9 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0   11
  8P LOSS WILD-TYPE    9  164
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              11               164
[1] 2 2
[1] FALSE

Clustering(51) Variable = 8Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     4   1
  8Q LOSS WILD-TYPE 183   6
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5               189 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                 6 
$`8Q LOSS MUTATED`
TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B3-3926 TCGA-F9-A7Q0 TCGA-G7-A8LC 
          87          223          307           10          262 

$`8Q LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
         379          516         1968            2          118            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
          26           67          595          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 
         108          510           14          200         1029          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379          309         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          452          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-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-A7VF 
        1670         1040          578          757           97            7 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
          36           13          208         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
        1059          765          446          786          194          197 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
        1967         1965         5925          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
          32          378          546           27          341          140 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
        2072          408          360         1726         2228          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 
         376            4          364          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         541          493          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
        2816          391          540          428         1457         1443 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1005          876          823         1973          578         1175 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C 
        1266          805         1469         1331          579          882 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
         224            2          186          219          181          399 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         205          106          104 

  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 
              223               554 
[1] "10.0 - 307.0 (223.0)" "2.0 - 5925.0 (554.0)"
[1] "hr=" "19" 
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED         3        1         1        1
  8Q LOSS WILD-TYPE     134       15        42       12
D51V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 3               134
  STAGE II                1                15
  STAGE III               1                42
  STAGE IV                1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  8Q LOSS MUTATED     4   1     1
  8Q LOSS WILD-TYPE 142  21    50
D51V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1                  4               142
  T2                  1                21
  T3+T4               1                50
[1] 3 2
[1] TRUE
[1] "dimension 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 39 18  4
D51V5, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                61 
       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-A47O        TCGA-B1-A655        TCGA-B1-A656 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B1-A657        TCGA-B9-7268        TCGA-BQ-5877        TCGA-BQ-5878 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5882        TCGA-BQ-5885 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5890        TCGA-BQ-5891 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7045 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7056 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-7058        TCGA-DW-7963        TCGA-DZ-6131        TCGA-F9-A8NY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F9-A97G        TCGA-G7-6789        TCGA-G7-6793        TCGA-G7-6795 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-A8LD        TCGA-GL-6846        TCGA-GL-7966 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GL-A59R        TCGA-GL-A9DC        TCGA-IA-A40U        TCGA-IA-A40Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IA-A83W        TCGA-J7-6720        TCGA-J7-8537        TCGA-KV-A74V 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-P4-A5E8        TCGA-P4-A5EA        TCGA-SX-A71R 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SP        TCGA-SX-A7SS        TCGA-Y8-A897 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-Y8-A8RZ 
"8Q LOSS WILD-TYPE" 
                   vv
clus                 M0  M1  MX
  8Q LOSS MUTATED     2   1   3
  8Q LOSS WILD-TYPE  86   7 109
D51V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               2                86
  M1               1                 7
  MX               3               109
[1] 3 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
  8Q LOSS MUTATED     3   3
  8Q LOSS WILD-TYPE  60 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    3
  8Q LOSS WILD-TYPE   60  155
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               3                60
  MALE                 3               155
[1] 2 2
[1] FALSE
D51V8, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                55 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8310        TCGA-A4-8311 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-8312        TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A4ZT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-7502        TCGA-G7-A4TM        TCGA-G7-A8LB        TCGA-G7-A8LD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-A8LE        TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-J7-8537        TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SX-A7SN        TCGA-SX-A7SO        TCGA-SX-A7SP        TCGA-SX-A7SQ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-SX-A7SU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D51V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     1
  8Q LOSS WILD-TYPE                                2     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           1     4
  8Q LOSS WILD-TYPE                        51   143
D51V10, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      1                51
  WHITE                                          4               143
[1] 4 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
  8Q LOSS MUTATED     0   6
  8Q LOSS WILD-TYPE   9 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    6
  8Q LOSS WILD-TYPE    9  169
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               6               169
[1] 2 2
[1] FALSE

Clustering(52) Variable = 9P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    18   3
  9P LOSS WILD-TYPE 169   4
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               21               173 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                3                 4 
$`9P LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B3-3926 
         554           21         1968           87           26          307 
TCGA-B9-4116 TCGA-B9-A69E TCGA-BQ-5888 TCGA-BQ-7048 TCGA-BQ-7056 TCGA-DZ-6131 
         627          452          403         2839          612         2429 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD 
          10          208         1059          446          262         1967 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-Y8-A896 
          62            4          186 

$`9P LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207          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-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         659          747          513          108          510           14 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
         200         1029          930         1049          379          309 
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-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1338          671           64          585          207            5 
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-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         233           29          364           84         3760         2948 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 
        1864         1533         1516          799          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-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        1240         2460         1856         1670         1040          578 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
         757           97            7           36           13         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
        1479         1194          765          786          194          197 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        1965         5925          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
         378          546           27          341          140         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
         408          360         1726         2228          167          511 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
         608          677          649          146          376          364 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          845          924          841 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
         616           11          369          541          493          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3035         2653         2584         2816          391          540 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
         428         1457         1443         1005          876          823 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
        1973          578         1175         1266          805         1469 
TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 
        1331          579          882          224            2          219 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         181          399          205          106          104 

  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 
              403               578 
[1] "4.0 - 2839.0 (403.0)" "2.0 - 5925.0 (578.0)"
[1] "hr=" "5.4"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED         6        0        13        5
  9P LOSS WILD-TYPE     131       16        30        8
D52V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 6               131
  STAGE II                0                16
  STAGE III              13                30
  STAGE IV                5                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  9P LOSS MUTATED     7   2    17
  9P LOSS WILD-TYPE 139  20    34
D52V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1                  7               139
  T2                  2                20
  T3+T4              17                34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  9P LOSS MUTATED    5  8  2
  9P LOSS WILD-TYPE 34 12  2
D52V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0               5                34
  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  12
  9P LOSS WILD-TYPE  80   5 100
D52V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0               8                80
  M1               3                 5
  MX              12               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    14  12
  9P LOSS WILD-TYPE  49 146
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     14   12
  9P LOSS WILD-TYPE   49  146
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              14                49
  MALE                12               146
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0     2
  9P LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                           2    21
  9P LOSS WILD-TYPE                        50   126
D52V10, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 3
  BLACK OR AFRICAN AMERICAN                      2                50
  WHITE                                         21               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"
D52V11, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     0  22
  9P LOSS WILD-TYPE   9 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      0   22
  9P LOSS WILD-TYPE    9  153
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              22               153
[1] 2 2
[1] FALSE

Clustering(53) Variable = 9Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    19   3
  9Q LOSS WILD-TYPE 168   4
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               22               172 
  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          452          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-G7-A8LC TCGA-IA-A40Y TCGA-J7-8537 TCGA-Y8-A896 
         262           62            4          186 

$`9Q LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
        1968            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-A47O TCGA-B1-A654 TCGA-B1-A655 
         223          659          747          513          108          510 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 
          14          200         1029          930          379          309 
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-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-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         233           29          364           84         3760         2948 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1864         1533         1516          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-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        2460         1856         1670         1040          578          757 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
           7           36           13         1575         1479         1194 
TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
         765          786          194          197         1967         1965 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
         546           27          341          140         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         360         1726         2228          167          511          608 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
         677          649          146          376          364          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          845          924          841          616 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
          11          369          541          493          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2653         2584         2816          391          540          428 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1457         1443         1005          876          823         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
         578         1175         1266          805         1469         1331 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 
         579          882          224            2          219          181 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         399          205          106          104 

  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 
            284.5             578.5 
[1] "4.0 - 2839.0 (284.5)" "2.0 - 5925.0 (578.5)"
[1] "hr=" "6.9"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED         7        1        14        4
  9Q LOSS WILD-TYPE     130       15        29        9
D53V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 7               130
  STAGE II                1                15
  STAGE III              14                29
  STAGE IV                4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  9Q LOSS MUTATED     8   1    18
  9Q LOSS WILD-TYPE 138  21    33
D53V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1                  8               138
  T2                  1                21
  T3+T4              18                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
  9Q LOSS MUTATED    4  7  2
  9Q LOSS WILD-TYPE 35 13  2
D53V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0               4                35
  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  12
  9Q LOSS WILD-TYPE  78   6 100
D53V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              10                78
  M1               2                 6
  MX              12               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    14  13
  9Q LOSS WILD-TYPE  49 145
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     14   13
  9Q LOSS WILD-TYPE   49  145
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              14                49
  MALE                13               145
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     2
  9Q LOSS WILD-TYPE                                2     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           3    21
  9Q LOSS WILD-TYPE                        49   126
D53V10, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 3
  BLACK OR AFRICAN AMERICAN                      3                49
  WHITE                                         21               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"
D53V11, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     0  21
  9Q LOSS WILD-TYPE   9 154
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      0   21
  9Q LOSS WILD-TYPE    9  154
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              21               154
[1] 2 2
[1] FALSE

Clustering(54) Variable = 10P LOSS MUTATION ANALYSIS
D54V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    10   2
  10P LOSS WILD-TYPE 177   5
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                12                182 
  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-G7-A8LC TCGA-GL-7966 TCGA-Q2-A5QZ 
         208          446          786          262          112          428 

$`10P LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
         379          516         1968            2          118            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
          67          595          223          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         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-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
         585          207            5          452          167           52 
TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
        2639          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-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        1240         2460         1856         1670         1040          578 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
         757           97           10            7           36           13 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-A4TM 
        1575         1479         1194         1059          765          194 
TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
         197         1967         1965         5925          393          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
          32          378          546           27          341          140 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
        2072          408          360         1726         2228          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 
         376            4          364          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         541          493          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          391          540         1457         1443         1005 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         876          823         1973          578         1175         1266 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
         805         1469         1331          579          882          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
           2          186          219          181          399          205 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         106          104 

  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 
               345                550 
[1] "26.0 - 2429.0 (345.0)" "2.0 - 5925.0 (550.0)" 
[1] "hr=" "7"  
D54V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED         3        0         7        2
  10P LOSS WILD-TYPE     134       16        36       11
D54V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  3                134
  STAGE II                 0                 16
  STAGE III                7                 36
  STAGE IV                 2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  10P LOSS MUTATED     4   1     8
  10P LOSS WILD-TYPE 142  21    43
D54V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                   4                142
  T2                   1                 21
  T3+T4                8                 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
  10P LOSS MUTATED    1  4  1
  10P LOSS WILD-TYPE 38 16  3
D54V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                1                 38
  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   9
  10P LOSS WILD-TYPE  87   7 103
D54V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0                1                 87
  M1                1                  7
  MX                9                103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     6   7
  10P LOSS WILD-TYPE  57 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      6    7
  10P LOSS WILD-TYPE   57  151
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                6                 57
  MALE                  7                151
[1] 2 2
[1] FALSE
D54V8, continuous
D54V9, continuous
[1] "Remove cluster labels:" "10P LOSS MUTATED"      
clus
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 2                 33 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-A69E         TCGA-F9-A97G 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A59T         TCGA-GL-A9DD 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-HE-A5NK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A83S         TCGA-IZ-A6M8 
"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-A7SR         TCGA-SX-A7SS         TCGA-WN-A9G9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RZ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     0
  10P LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           4     9
  10P LOSS WILD-TYPE                        48   138
D54V10, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       4                 48
  WHITE                                           9                138
[1] 4 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
  10P LOSS MUTATED     0  11
  10P LOSS WILD-TYPE   9 164
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      0   11
  10P LOSS WILD-TYPE    9  164
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               11                164
[1] 2 2
[1] FALSE

Clustering(55) Variable = 10Q LOSS MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    10   2
  10Q LOSS WILD-TYPE 177   5
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                12                182 
  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-G7-A8LC TCGA-GL-7966 TCGA-J7-8537 TCGA-Q2-A5QZ 
         446          786          262          112            4          428 

$`10Q LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
         379          516         1968            2          118            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
          67          595          223          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         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          452          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-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-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-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
          13         1575         1479         1194         1059          765 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         194          197         1967         1965         5925          393 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
         841           32          378          546           27          341 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         140         2072          408          360         1726         2228 
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-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         146          376          364          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         541          493          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          391          540         1457         1443         1005 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         876          823         1973          578         1175         1266 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
         805         1469         1331          579          882          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
           2          186          219          181          399          205 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         106          104 

  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 
               235                566 
[1] "4.0 - 2429.0 (235.0)" "2.0 - 5925.0 (566.0)"
[1] "hr=" "7.6"
D55V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED         3        0         8        2
  10Q LOSS WILD-TYPE     134       16        35       11
D55V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  3                134
  STAGE II                 0                 16
  STAGE III                8                 35
  STAGE IV                 2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  10Q LOSS MUTATED     4   0     9
  10Q LOSS WILD-TYPE 142  22    42
D55V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                   4                142
  T2                   0                 22
  T3+T4                9                 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
  10Q LOSS MUTATED    1  5  1
  10Q LOSS WILD-TYPE 38 15  3
D55V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                1                 38
  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   9
  10Q LOSS WILD-TYPE  86   7 103
D55V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                2                 86
  M1                1                  7
  MX                9                103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     6   7
  10Q LOSS WILD-TYPE  57 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      6    7
  10Q LOSS WILD-TYPE   57  151
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                6                 57
  MALE                  7                151
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, continuous
[1] "Remove cluster labels:" "10Q LOSS MUTATED"      
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                 33 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-A69E         TCGA-F9-A97G 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A59T         TCGA-GL-A9DD 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-HE-A5NK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A83S         TCGA-IZ-A6M8 
"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-A7SR         TCGA-SX-A7SS         TCGA-WN-A9G9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RZ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     1
  10Q LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                           3     9
  10Q LOSS WILD-TYPE                        49   138
D55V10, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       3                 49
  WHITE                                           9                138
[1] 4 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
  10Q LOSS MUTATED     0  11
  10Q LOSS WILD-TYPE   9 164
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      0   11
  10Q LOSS WILD-TYPE    9  164
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               11                164
[1] 2 2
[1] FALSE

Clustering(56) Variable = 11P LOSS MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED     9   3
  11P LOSS WILD-TYPE 178   4
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                12                182 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 3                  4 
$`11P LOSS MUTATED`
TCGA-A4-7287 TCGA-B1-7332 TCGA-B3-4104 TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 
          21          223         1049           64          586          270 
TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y TCGA-Y8-A896 TCGA-Y8-A8S1 
         208          786         1967           62          186          104 

$`11P LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207          554          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
         516         1968            2          118           87            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
          26           67          595          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
         930          379          309         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-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
         585          207            5          452          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-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-F9-A97G 
         757           97           10            7           36           13 
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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         194          197          262         1965         5925          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
         112          841           32          378          546           27 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         341          140         2072          408          360         1726 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 
        2228          167          511          608          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         146          376            4          364          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          845          924          841          616           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        2584         2816          391          540          428         1457 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1443         1005          876          823         1973          578 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 
        1175         1266          805         1469         1331          579 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
         882          224            2          219          181          399 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 
         205          106 

  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 
             215.5              550.0 
[1] "21.0 - 1967.0 (215.5)" "2.0 - 5925.0 (550.0)" 
[1] "hr=" "20" 
D56V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         4        2         6        2
  11P LOSS WILD-TYPE     133       14        37       11
D56V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  4                133
  STAGE II                 2                 14
  STAGE III                6                 37
  STAGE IV                 2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  11P LOSS MUTATED     4   2     8
  11P LOSS WILD-TYPE 142  20    43
D56V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                   4                142
  T2                   2                 20
  T3+T4                8                 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 38 17  3
D56V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                1                 38
  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   8
  11P LOSS WILD-TYPE  84   7 104
D56V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                4                 84
  M1                1                  7
  MX                8                104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     5   9
  11P LOSS WILD-TYPE  58 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5    9
  11P LOSS WILD-TYPE   58  149
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                5                 58
  MALE                  9                149
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     0
  11P LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           3     9
  11P LOSS WILD-TYPE                        49   138
D56V10, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       3                 49
  WHITE                                           9                138
[1] 4 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
  11P LOSS MUTATED     0  10
  11P LOSS WILD-TYPE   9 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   10
  11P LOSS WILD-TYPE    9  165
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               10                165
[1] 2 2
[1] FALSE

Clustering(57) Variable = 11Q LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    10   2
  11Q LOSS WILD-TYPE 177   5
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                12                182 
  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-F9-A97G TCGA-G7-6789 TCGA-G7-7502 TCGA-IA-A40Y TCGA-J7-8537 TCGA-Y8-A896 
          13          208          786           62            4          186 

$`11Q LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         379          516         1968            2          118           87 
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-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         513          108          510           14          200         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
         307          930         1049          379          309         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-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1338          671          585          207            5          452 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
         167           52         2639         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 
         792          921          792          771          403           29 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
         364           84         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-A4TM 
        1479         1194         1059          765          446          194 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         197          262         1967         1965         5925          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
         112          841           32          378          546           27 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         341          140         2072          408          360         1726 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 
        2228          167          511          608          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         146          376          364          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         541          493          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
        2816          391          540          428         1457         1443 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1005          876          823         1973          578         1175 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C 
        1266          805         1469         1331          579          882 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
         224            2          219          181          399          205 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         106          104 

  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 
             215.5              566.0 
[1] "4.0 - 3760.0 (215.5)" "2.0 - 5925.0 (566.0)"
[1] "hr=" "7.9"
D57V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         2        1         9        4
  11Q LOSS WILD-TYPE     135       15        34        9
D57V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  2                135
  STAGE II                 1                 15
  STAGE III                9                 34
  STAGE IV                 4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  11Q LOSS MUTATED     2   1    13
  11Q LOSS WILD-TYPE 144  21    38
D57V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                   2                144
  T2                   1                 21
  T3+T4               13                 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    3  4  2
  11Q LOSS WILD-TYPE 36 16  2
D57V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                3                 36
  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     7   2   6
  11Q LOSS WILD-TYPE  81   6 106
D57V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                7                 81
  M1                2                  6
  MX                6                106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     6  10
  11Q LOSS WILD-TYPE  57 148
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      6   10
  11Q LOSS WILD-TYPE   57  148
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                6                 57
  MALE                 10                148
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     2
  11Q LOSS WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           3     9
  11Q LOSS WILD-TYPE                        49   138
D57V10, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                       3                 49
  WHITE                                           9                138
[1] 4 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
  11Q LOSS MUTATED     0  11
  11Q LOSS WILD-TYPE   9 164
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   11
  11Q LOSS WILD-TYPE    9  164
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               11                164
[1] 2 2
[1] FALSE

Clustering(58) Variable = 13Q LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    14   3
  13Q LOSS WILD-TYPE 173   4
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                17                177 
  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          309         2639 
TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LC 
          84           97           10          208          786          262 
TCGA-G7-A8LD TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ 
        1967          112           62            4          428 

$`13Q LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207          554          493            3          582           27 
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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
        1968            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-A47O TCGA-B1-A654 
         595          223          659          747          513          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
         510           14          200         1029          930         1049 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
         379         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-5876 
         207            5          452          167           52          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-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
           7           36           13         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE 
        1059          765          446          194          197         1965 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
        5925          393          841           32          378          546 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          27          341          140         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 
        1726         2228          167          511          608          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         649          146          376          364          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          845          924          841          616           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
        2584         2816          391          540         1457         1443 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1005          876          823         1973          578         1175 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C 
        1266          805         1469         1331          579          882 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
         224            2          186          219          181          399 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         205          106          104 

  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 
               112                579 
[1] "4.0 - 2639.0 (112.0)" "2.0 - 5925.0 (579.0)"
[1] "hr=" "10" 
D58V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED         6        1        11        3
  13Q LOSS WILD-TYPE     131       15        32       10
D58V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  6                131
  STAGE II                 1                 15
  STAGE III               11                 32
  STAGE IV                 3                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  13Q LOSS MUTATED     6   2    13
  13Q LOSS WILD-TYPE 140  20    38
D58V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                   6                140
  T2                   2                 20
  T3+T4               13                 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
  13Q LOSS MUTATED    2  7  2
  13Q LOSS WILD-TYPE 37 13  2
D58V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                2                 37
  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 13
  13Q LOSS WILD-TYPE 81  7 99
D58V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0                7                 81
  M1                1                  7
  MX               13                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    14   7
  13Q LOSS WILD-TYPE  49 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     14    7
  13Q LOSS WILD-TYPE   49  151
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               14                 49
  MALE                  7                151
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, continuous
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 33 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-A44B         TCGA-B9-A69E 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-A8LB         TCGA-G7-A8LE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A59T         TCGA-GL-A9DD 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-HE-A5NK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A83S         TCGA-IZ-A6M8 
"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-A7SR         TCGA-SX-A7SS         TCGA-WN-A9G9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RZ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  0     2
  13Q LOSS WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                           4    13
  13Q LOSS WILD-TYPE                        48   134
D58V10, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                       4                 48
  WHITE                                          13                134
[1] 4 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
  13Q LOSS MUTATED     1  16
  13Q LOSS WILD-TYPE   8 159
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   16
  13Q LOSS WILD-TYPE    8  159
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               16                159
[1] 2 2
[1] FALSE

Clustering(59) Variable = 14Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    31   4
  14Q LOSS WILD-TYPE 156   3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                35                159 
  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-A8LC TCGA-G7-A8LD TCGA-GL-8500 TCGA-HE-A5NK TCGA-IA-A40U 
         786          262         1967          841         2228          511 
TCGA-IA-A40Y TCGA-MH-A854 TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-WN-A9G9 
          62           11          391          428          579 

$`14Q LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
         207          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-A57E TCGA-A4-A5XZ 
         600          436          379          516         1968            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-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
          67          595          659          747          513          108 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
          14          200         1029          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
         309         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-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 
         452          167           52         2639          270         1938 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 
        1454         1242          792          792          771          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-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        1240         1856         1670         1040          578          757 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
           7           36           13         1575         1479         1194 
TCGA-G7-6797 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         765          194          197         1965         5925          393 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
         112           32          378          546           27          341 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
         140         2072          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          376            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         364          885          161         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
         841          616          369          541          493          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-SX-A71R 
        3035         2653         2584         2816          540         1457 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1443         1005          876          823         1973          578 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-AB4C 
        1175         1266          805         1469         1331          882 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
         224            2          186          219          181          399 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         205          106          104 

  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 
               428                578 
[1] "3.0 - 2460.0 (428.0)" "2.0 - 5925.0 (578.0)"
[1] "hr=" "6.2"
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED        16        3        11        6
  14Q LOSS WILD-TYPE     121       13        32        7
D59V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                 16                121
  STAGE II                 3                 13
  STAGE III               11                 32
  STAGE IV                 6                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  14Q LOSS MUTATED    18   4    17
  14Q LOSS WILD-TYPE 128  18    34
D59V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                  18                128
  T2                   4                 18
  T3+T4               17                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  14Q LOSS MUTATED    7  8  3
  14Q LOSS WILD-TYPE 32 12  1
D59V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                7                 32
  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   12  3 22
  14Q LOSS WILD-TYPE 76  5 90
D59V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0               12                 76
  M1                3                  5
  MX               22                 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"
D59V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    18  21
  14Q LOSS WILD-TYPE  45 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     18   21
  14Q LOSS WILD-TYPE   45  137
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               18                 45
  MALE                 21                137
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0     1
  14Q LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                           9    26
  14Q LOSS WILD-TYPE                        43   121
D59V10, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       9                 43
  WHITE                                          26                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"
D59V11, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     1  32
  14Q LOSS WILD-TYPE   8 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   32
  14Q LOSS WILD-TYPE    8  143
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               32                143
[1] 2 2
[1] FALSE

Clustering(60) Variable = 15Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    16   3
  15Q LOSS WILD-TYPE 171   4
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                19                175 
  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-G7-A8LC TCGA-GL-6846 TCGA-GL-7966 TCGA-HE-A5NK TCGA-PJ-A5Z8 TCGA-Y8-A896 
         262         5925          112         2228          391          186 
TCGA-Y8-A8S1 
         104 

$`15Q LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207           21          493          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
        1968            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-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
         223          659          747          513          108          510 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
          14          200         1029          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
         309         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-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
           5          452          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-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
           7           36           13         1575         1479         1194 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
         765          446          194          197         1967         1965 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
         393          841           32          378          546           27 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         341          140         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          376            4          364          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          845          924          841          616           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
        2584         2816          540          428         1457         1443 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1005          876          823         1973          578         1175 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C 
        1266          805         1469         1331          579          882 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
         224            2          219          181          399          205 
TCGA-Y8-A8S0 
         106 

  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 
               208                578 
[1] "3.0 - 5925.0 (208.0)" "2.0 - 3950.0 (578.0)"
[1] "hr=" "7.6"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED         8        1         9        4
  15Q LOSS WILD-TYPE     129       15        34        9
D60V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  8                129
  STAGE II                 1                 15
  STAGE III                9                 34
  STAGE IV                 4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  15Q LOSS MUTATED    10   1    13
  15Q LOSS WILD-TYPE 136  21    38
D60V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                  10                136
  T2                   1                 21
  T3+T4               13                 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
  15Q LOSS MUTATED    3  7  1
  15Q LOSS WILD-TYPE 36 13  3
D60V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                3                 36
  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    10   2  11
  15Q LOSS WILD-TYPE  78   6 101
D60V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0               10                 78
  M1                2                  6
  MX               11                101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     9  15
  15Q LOSS WILD-TYPE  54 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      9   15
  15Q LOSS WILD-TYPE   54  143
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                9                 54
  MALE                 15                143
[1] 2 2
[1] FALSE
D60V8, continuous
D60V9, continuous
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                 33 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-A44B         TCGA-B9-A69E 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-A8LB         TCGA-G7-A8LD 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-7773         TCGA-GL-A59T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-HE-A5NJ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A83S         TCGA-IZ-A6M8 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-PJ-A5Z9         TCGA-Q2-A5QZ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SR         TCGA-SX-A7SS 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-Y8-A894         TCGA-Y8-A8RZ 
"15Q LOSS WILD-TYPE" "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     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           3    16
  15Q LOSS WILD-TYPE                        49   131
D60V10, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       3                 49
  WHITE                                          16                131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     1  18
  15Q LOSS WILD-TYPE   8 157
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1   18
  15Q LOSS WILD-TYPE    8  157
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               18                157
[1] 2 2
[1] FALSE

Clustering(61) Variable = 16P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     1   0
  16P LOSS WILD-TYPE 186   7
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                193 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 0                  7 
$`16P LOSS MUTATED`
TCGA-A4-7287 
          21 

$`16P LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207          554          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
         516         1968            2          118           87            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          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-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         513          108          510           14          200         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
         307          930         1049          379          309         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 
         452          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-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
          97           10            7           36           13          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-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
         786          194          197          262         1967         1965 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
         546           27          341          140         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         360         1726         2228          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          376            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         364          885          161         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
         841          616           11          369          541          493 
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 
         540          428         1457         1443         1005          876 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR 
         823         1973          578         1175         1266          805 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
        1469         1331          579          882          224            2 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
         186          219          181          399          205          106 
TCGA-Y8-A8S1 
         104 

  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                541 
[1] "21.0 - 21.0 (21.0)"   "2.0 - 5925.0 (541.0)"
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         1        0         2        1
  16P LOSS WILD-TYPE     136       16        41       12
D61V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  1                136
  STAGE II                 0                 16
  STAGE III                2                 41
  STAGE IV                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  16P LOSS MUTATED     1   0     3
  16P LOSS WILD-TYPE 145  22    48
D61V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                   1                145
  T2                   0                 22
  T3+T4                3                 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
  16P LOSS MUTATED    1  0  1
  16P LOSS WILD-TYPE 38 20  3
D61V5, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 61 
        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-A47O         TCGA-B1-A655 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-A656         TCGA-B1-A657         TCGA-B9-7268 
"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-5885         TCGA-BQ-5887 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7045         TCGA-BQ-7048 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7056 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-DW-7963         TCGA-DZ-6131 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F9-A8NY         TCGA-F9-A97G         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-GL-A9DC         TCGA-IA-A40U         TCGA-IA-A40Y 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A83W         TCGA-J7-6720         TCGA-J7-8537 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KV-A74V         TCGA-P4-A5E6         TCGA-P4-A5E8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-P4-A5EA         TCGA-SX-A71R         TCGA-SX-A7SM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SS         TCGA-Y8-A897 
"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  86   8 110
D61V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0                2                 86
  M1                0                  8
  MX                2                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3   1
  16P LOSS WILD-TYPE  60 157
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    1
  16P LOSS WILD-TYPE   60  157
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                3                 60
  MALE                  1                157
[1] 2 2
[1] FALSE
D61V8, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 55 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8310 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A4ZT         TCGA-A4-A57E 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6796         TCGA-G7-6797 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-G7-A4TM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LC         TCGA-G7-A8LD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-IA-A40U         TCGA-IA-A40X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-8537         TCGA-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-A7SR         TCGA-SX-A7SS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SU 
"16P LOSS WILD-TYPE" 
D61V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     0
  16P LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           0     2
  16P LOSS WILD-TYPE                        52   145
D61V10, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                204 
        TCGA-2K-A9WE         TCGA-A4-7286         TCGA-A4-7288 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7584         TCGA-A4-7585 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7732         TCGA-A4-7734         TCGA-A4-7828 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7915         TCGA-A4-7996         TCGA-A4-7997 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8312         TCGA-A4-8515         TCGA-A4-8516 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8517         TCGA-A4-8518         TCGA-A4-8630 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A4ZT         TCGA-A4-A57E 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A5Y0 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A5Y1         TCGA-A4-A6HP         TCGA-A4-A772 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-7173         TCGA-AL-A5DJ         TCGA-AT-A5NU 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B1-A47M 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-A47N         TCGA-B1-A47O         TCGA-B1-A654 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-A655         TCGA-B1-A656         TCGA-B1-A657 
"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-F9-A97G         TCGA-G7-6789 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6795 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-G7-A4TM         TCGA-G7-A8LB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-A8LC         TCGA-G7-A8LD         TCGA-G7-A8LE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7773         TCGA-GL-7966 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-GL-A9DC         TCGA-GL-A9DD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-A9DE         TCGA-IA-A40U         TCGA-IA-A40X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IA-A83S         TCGA-IA-A83T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A83W         TCGA-IZ-8195         TCGA-IZ-8196 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IZ-A6M8         TCGA-IZ-A6M9         TCGA-J7-6720 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-J7-8537         TCGA-KV-A6GD         TCGA-KV-A6GE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KV-A74V         TCGA-MH-A55W         TCGA-MH-A55Z 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MH-A560         TCGA-MH-A561         TCGA-MH-A562 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A855         TCGA-MH-A856 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MH-A857         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-A7SR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-WN-A9G9         TCGA-WN-AB4C 
"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-A897         TCGA-Y8-A898         TCGA-Y8-A8RY 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-Y8-A8S0         TCGA-Y8-A8S1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D61V11, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     0   2
  16P LOSS WILD-TYPE   9 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    2
  16P LOSS WILD-TYPE    9  173
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                2                173
[1] 2 2
[1] FALSE

Clustering(62) Variable = 16Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED     1   2
  16Q LOSS WILD-TYPE 186   5
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 3                191 
  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-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207          554          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
         516         1968            2          118            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-A47O 
          67          595          223          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         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          452 
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-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-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
          10            7           36           13          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-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         194          197          262         1965         5925          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
         112          841           32          378          546           27 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         341          140         2072          408          360         1726 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        2228          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          376            4          364          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          845          924          841          616 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
          11          369          541          493          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2653         2584         2816          391          540          428 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1457         1443         1005          876          823         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
         578         1175         1266          805         1469         1331 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
         579          882          224            2          186          219 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         181          399          205          106          104 

  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                541 
[1] "21.0 - 1967.0 (87.0)" "2.0 - 5925.0 (541.0)"
[1] "hr=" "31" 
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         1        0         4        1
  16Q LOSS WILD-TYPE     136       16        39       12
D62V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  1                136
  STAGE II                 0                 16
  STAGE III                4                 39
  STAGE IV                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  16Q LOSS MUTATED     2   0     4
  16Q LOSS WILD-TYPE 144  22    47
D62V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                   2                144
  T2                   0                 22
  T3+T4                4                 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
  16Q LOSS MUTATED    1  2  1
  16Q LOSS WILD-TYPE 38 18  3
D62V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                1                 38
  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  86   8 108
D62V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0                2                 86
  M1                0                  8
  MX                4                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     3   3
  16Q LOSS WILD-TYPE  60 155
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    3
  16Q LOSS WILD-TYPE   60  155
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                3                 60
  MALE                  3                155
[1] 2 2
[1] FALSE
D62V8, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 54 
        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-G7-A8LB         TCGA-G7-A8LC         TCGA-G7-A8LE 
"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-A7SR         TCGA-SX-A7SS         TCGA-SX-A7SU 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D62V9, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 34 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-A44B         TCGA-B9-A69E 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-A8LB         TCGA-G7-A8LE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A59T         TCGA-GL-A9DD 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-HE-A5NK 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A83S         TCGA-IZ-A6M8 
"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-A7SR         TCGA-SX-A7SS 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-Y8-A894         TCGA-Y8-A896 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ 
"16Q LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     0
  16Q LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           0     4
  16Q LOSS WILD-TYPE                        52   143
D62V10, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       0                 52
  WHITE                                           4                143
[1] 4 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
  16Q LOSS MUTATED     0   4
  16Q LOSS WILD-TYPE   9 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0    4
  16Q LOSS WILD-TYPE    9  171
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                4                171
[1] 2 2
[1] FALSE

Clustering(63) Variable = 17P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED     3   0
  17P LOSS WILD-TYPE 184   7
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                191 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 0                  7 
$`17P LOSS MUTATED`
TCGA-A4-7287 TCGA-A4-7915 TCGA-A4-A57E 
          21            7         1968 

$`17P LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207          554          493            3          582           27 
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-A47O TCGA-B1-A654 
         595          223          659          747          513          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         510           14          200         1029          307          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379          309         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          452          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-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-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
           7           36           13          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          194 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         197          262         1967         1965         5925          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
         112          841           32          378          546           27 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         341          140         2072          408          360         1726 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        2228          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          376            4          364          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          845          924          841          616 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
          11          369          541          493          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2653         2584         2816          391          540          428 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1457         1443         1005          876          823         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
         578         1175         1266          805         1469         1331 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
         579          882          224            2          186          219 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         181          399          205          106          104 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                  2 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              1968               5925 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                21                541 
[1] "7.0 - 1968.0 (21.0)"  "2.0 - 5925.0 (541.0)"
[1] "hr="     "9500000"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED         1        1         2        3
  17P LOSS WILD-TYPE     136       15        41       10
D63V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  1                136
  STAGE II                 1                 15
  STAGE III                2                 41
  STAGE IV                 3                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  17P LOSS MUTATED     1   2     4
  17P LOSS WILD-TYPE 145  20    47
D63V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                   1                145
  T2                   2                 20
  T3+T4                4                 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
  17P LOSS MUTATED    2  1  2
  17P LOSS WILD-TYPE 37 19  2
D63V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                2                 37
  N1                1                 19
  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
  17P LOSS MUTATED     2   2   3
  17P LOSS WILD-TYPE  86   6 109
D63V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0                2                 86
  M1                2                  6
  MX                3                109
[1] 3 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
  17P LOSS MUTATED     4   3
  17P LOSS WILD-TYPE  59 155
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4    3
  17P LOSS WILD-TYPE   59  155
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                4                 59
  MALE                  3                155
[1] 2 2
[1] FALSE
D63V8, continuous
D63V9, continuous
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 1                 34 
        TCGA-A4-A48D         TCGA-A4-A5Y0         TCGA-B1-A654 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-A44B         TCGA-B9-A69E         TCGA-F9-A97G 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A59T         TCGA-GL-A9DD 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-HE-A5NK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A83S         TCGA-IZ-A6M8 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E7 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-P4-A5EB         TCGA-PJ-A5Z9         TCGA-Q2-A5QZ 
"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-A7SR         TCGA-SX-A7SS 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-Y8-A894         TCGA-Y8-A896 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ 
"17P LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0     0
  17P LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                           1     5
  17P LOSS WILD-TYPE                        51   142
D63V10, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       1                 51
  WHITE                                           5                142
[1] 4 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
  17P LOSS MUTATED     0   6
  17P LOSS WILD-TYPE   9 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      0    6
  17P LOSS WILD-TYPE    9  169
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                6                169
[1] 2 2
[1] FALSE

Clustering(64) Variable = 18P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    24   4
  18P LOSS WILD-TYPE 163   3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                28                166 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                  3 
$`18P LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-8310 TCGA-A4-A57E TCGA-AL-A5DJ TCGA-B1-7332 
         554           21          780         1968           26          223 
TCGA-B1-A656 TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5887 TCGA-BQ-5894 
          14          307          627          270          771           84 
TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7059 TCGA-DW-7840 TCGA-EV-5903 TCGA-F9-A4JJ 
        3760         2839          232          114          757           97 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-GL-7773 TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 
          10          208          393          112           62            4 
TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SO TCGA-Y8-A8S1 
         428         1973         1175          104 

$`18P LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207          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-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-A47M 
         923          763         1357           67          595          659 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 
         747          513          108          510          200         1029 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         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-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
          64          585          207            5          452          167 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
          52         2639          586         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
         792          921          792          403          233           29 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
         364         2948         1864         1533         1516          799 
TCGA-BQ-7056 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         612          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 
        3950         1093         1142          744          419          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-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
        1040          578            7           36           13         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-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
         194          197          262         1967         1965         5925 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
         841           32          378          546           27          341 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         140         2072          408          360         1726         2228 
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 
         376          364          885          161         1043          845 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
         924          841          616           11          369          541 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         493          148         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         391          540         1457         1443         1005          876 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
         823          578         1266          805         1469         1331 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
         579          882          224            2          186          219 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
         181          399          205          106 

  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 
             251.0              578.5 
[1] "4.0 - 3760.0 (251.0)" "2.0 - 5925.0 (578.5)"
[1] "hr=" "7.7"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED        10        1        15        5
  18P LOSS WILD-TYPE     127       15        28        8
D64V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                 10                127
  STAGE II                 1                 15
  STAGE III               15                 28
  STAGE IV                 5                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  18P LOSS MUTATED    10   3    20
  18P LOSS WILD-TYPE 136  19    31
D64V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                  10                136
  T2                   3                 19
  T3+T4               20                 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
  18P LOSS MUTATED    5  8  2
  18P LOSS WILD-TYPE 34 12  2
D64V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                5                 34
  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 13
  18P LOSS WILD-TYPE 74  4 99
D64V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               14                 74
  M1                4                  4
  MX               13                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    15  18
  18P LOSS WILD-TYPE  48 140
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     15   18
  18P LOSS WILD-TYPE   48  140
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               15                 48
  MALE                 18                140
[1] 2 2
[1] FALSE
D64V8, continuous
D64V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0     2
  18P LOSS WILD-TYPE                                2     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                           7    21
  18P LOSS WILD-TYPE                        45   126
D64V10, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                       7                 45
  WHITE                                          21                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"
D64V11, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     1  25
  18P LOSS WILD-TYPE   8 150
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1   25
  18P LOSS WILD-TYPE    8  150
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               25                150
[1] 2 2
[1] FALSE

Clustering(65) Variable = 18Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    25   6
  18Q LOSS WILD-TYPE 162   1
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                31                163 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 6                  1 
$`18Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-8310 TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-A5DJ 
         554           21          780         1968           87           26 
TCGA-B1-7332 TCGA-B1-A656 TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5887 
         223           14          307          627          270          771 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7059 TCGA-DW-7840 TCGA-EV-5903 
          84         3760         2839          232          114          757 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-A8LD TCGA-GL-7773 
          97           10           13          208         1967          393 
TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SO 
         112           62            4          428         1973         1175 
TCGA-Y8-A8S1 
         104 

$`18Q LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207          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-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
         763         1357           67          595          659          747 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 
         513          108          510          200         1029          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379          309         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-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
         585          207            5          452          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-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         921          792          403          233           29          364 
TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2948         1864         1533         1516          799          612 
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-7841 TCGA-DW-7842 
        1093         1142          744          419          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-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
         578            7           36         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
        1059          765          446          786          194          197 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
         262         1965         5925          841           32          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
         546           27          341          140         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         360         1726         2228          167          511          608 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
         677          649          146          376          364          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          845          924          841          616 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
          11          369          541          493          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R 
        2653         2584         2816          391          540         1457 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SQ 
        1443         1005          876          823          578         1266 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
         805         1469         1331          579          882          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
           2          186          219          181          399          205 
TCGA-Y8-A8S0 
         106 

  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                579 
[1] "4.0 - 3760.0 (232.0)" "2.0 - 5925.0 (579.0)"
[1] "hr=" "32" 
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED        10        1        18        5
  18Q LOSS WILD-TYPE     127       15        25        8
D65V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                 10                127
  STAGE II                 1                 15
  STAGE III               18                 25
  STAGE IV                 5                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  18Q LOSS MUTATED    11   3    22
  18Q LOSS WILD-TYPE 135  19    29
D65V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                  11                135
  T2                   3                 19
  T3+T4               22                 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
  18Q LOSS MUTATED    6 10  2
  18Q LOSS WILD-TYPE 33 10  2
D65V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                6                 33
  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   15  4 15
  18Q LOSS WILD-TYPE 73  4 97
D65V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               15                 73
  M1                4                  4
  MX               15                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    15  21
  18Q LOSS WILD-TYPE  48 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     15   21
  18Q LOSS WILD-TYPE   48  137
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               15                 48
  MALE                 21                137
[1] 2 2
[1] FALSE
D65V8, continuous
D65V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0     3
  18Q LOSS WILD-TYPE                                2     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                           7    23
  18Q LOSS WILD-TYPE                        45   124
D65V10, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                  2
  BLACK OR AFRICAN AMERICAN                       7                 45
  WHITE                                          23                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"
D65V11, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     1  28
  18Q LOSS WILD-TYPE   8 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1   28
  18Q LOSS WILD-TYPE    8  147
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               28                147
[1] 2 2
[1] FALSE

Clustering(66) Variable = 19P LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    10   3
  19P LOSS WILD-TYPE 177   4
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                13                181 
  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 
         428 

$`19P LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8515 
           7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
        1968            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-A47O TCGA-B1-A654 TCGA-B1-A655 
         595          659          747          513          108          510 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
          14          200         1029          307          930         1049 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
         379          309         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-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
         207            5          452          167           52         2639 
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-5892 TCGA-BQ-5894 
         792          771          403          233          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-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
          97           10            7           36           13         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
        1479         1194         1059          765          446          194 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         197          262         1965         5925          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
         841           32          378          546           27          341 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         140         2072          408          360         1726         2228 
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 
         376            4          364          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED 
         541          493          148         3035         2653         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         391          540         1457         1443         1005          876 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR 
         823         1973          578         1175         1266          805 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
        1469         1331          579          882          224            2 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
         186          219          181          399          205          106 
TCGA-Y8-A8S1 
         104 

  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 
               428                541 
[1] "29.0 - 2584.0 (428.0)" "2.0 - 5925.0 (541.0)" 
[1] "hr=" "10" 
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P LOSS MUTATED         3        1         7        1
  19P LOSS WILD-TYPE     134       15        36       12
D66V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  3                134
  STAGE II                 1                 15
  STAGE III                7                 36
  STAGE IV                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  19P LOSS MUTATED     4   1     8
  19P LOSS WILD-TYPE 142  21    43
D66V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                   4                142
  T2                   1                 21
  T3+T4                8                 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
  19P LOSS MUTATED    1  3  1
  19P LOSS WILD-TYPE 38 17  3
D66V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                1                 38
  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  86   8 103
D66V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0                2                 86
  M1                0                  8
  MX                9                103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     5   8
  19P LOSS WILD-TYPE  58 150
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      5    8
  19P LOSS WILD-TYPE   58  150
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                5                 58
  MALE                  8                150
[1] 2 2
[1] FALSE
D66V8, continuous
D66V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0     0
  19P LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           3    10
  19P LOSS WILD-TYPE                        49   137
D66V10, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       3                 49
  WHITE                                          10                137
[1] 4 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
  19P LOSS MUTATED     0  12
  19P LOSS WILD-TYPE   9 163
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   12
  19P LOSS WILD-TYPE    9  163
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               12                163
[1] 2 2
[1] FALSE

Clustering(67) Variable = 19Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED     8   4
  19Q LOSS WILD-TYPE 179   3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                182 
  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          428 

$`19Q LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8515 
           7           49            2          140          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
        1968            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-A47O TCGA-B1-A654 TCGA-B1-A655 
         595          659          747          513          108          510 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
          14          200         1029          307          930         1049 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
         379          309         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-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
         207            5          452          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-5892 
         921          792          771          403          233          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-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
         757           10            7           36           13         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
        1479         1194         1059          765          446          194 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         197          262         1965         5925          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
         841           32          378          546           27          341 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         140         2072          408          360         1726         2228 
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 
         376            4          364          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         541          493          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          391          540         1457         1443         1005 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         876          823         1973          578         1175         1266 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
         805         1469         1331          579          882          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
           2          186          219          181          399          205 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         106          104 

  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 
             215.5              562.0 
[1] "29.0 - 1967.0 (215.5)" "2.0 - 5925.0 (562.0)" 
[1] "hr=" "41" 
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         1        1         8        1
  19Q LOSS WILD-TYPE     136       15        35       12
D67V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  1                136
  STAGE II                 1                 15
  STAGE III                8                 35
  STAGE IV                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  19Q LOSS MUTATED     2   1     9
  19Q LOSS WILD-TYPE 144  21    42
D67V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                   2                144
  T2                   1                 21
  T3+T4                9                 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
  19Q LOSS MUTATED    1  3  1
  19Q LOSS WILD-TYPE 38 17  3
D67V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                1                 38
  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  87   8 103
D67V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                1                 87
  M1                0                  8
  MX                9                103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     6   6
  19Q LOSS WILD-TYPE  57 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6    6
  19Q LOSS WILD-TYPE   57  152
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                6                 57
  MALE                  6                152
[1] 2 2
[1] FALSE
D67V8, continuous
D67V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     0
  19Q LOSS WILD-TYPE                                2     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           4     8
  19Q LOSS WILD-TYPE                        48   139
D67V10, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       4                 48
  WHITE                                           8                139
[1] 4 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
  19Q LOSS MUTATED     0  11
  19Q LOSS WILD-TYPE   9 164
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   11
  19Q LOSS WILD-TYPE    9  164
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               11                164
[1] 2 2
[1] FALSE

Clustering(68) Variable = 21Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    28   2
  21Q LOSS WILD-TYPE 159   5
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                30                164 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                  5 
$`21Q LOSS MUTATED`
TCGA-A4-7288 TCGA-A4-8516 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-AL-3468 
         493           23          516         1968            2         1636 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B9-4114 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
        1029          307          857           64          585          207 
TCGA-BQ-5875 TCGA-BQ-5885 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7061 TCGA-DZ-6134 
        2639          921          233           84          218         1856 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6796 TCGA-GL-7966 TCGA-GL-A9DC 
          97           10          208         1059          112           27 
TCGA-HE-A5NF TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GE TCGA-KV-A74V TCGA-PJ-A5Z9 
        2072          511           62          885          161          540 

$`21Q LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207          554           21            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-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A5Y0 
         709          597          600          436          379          118 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
          87            4         1778          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-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         747          513          108          510           14          200 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4115 
         930         1049          379          309         1536          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-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 
           5          452          167           52          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-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 
         403           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-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-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        1240         2429         2460         1670         1040          578 
TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
         757            7           36           13         1575         1479 
TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
        1194          765          446          786          194          197 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
         262         1967         1965         5925          393          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH 
          32          378          546          341          140          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X TCGA-IZ-8195 
         360         1726         2228          167          608          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A55W 
         649          146          376            4          364         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         541          493          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          391          428         1457         1443         1005 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         876          823         1973          578         1175         1266 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
         805         1469         1331          579          882          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
           2          186          219          181          399          205 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         106          104 

  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 
               400                578 
[1] "2.0 - 2639.0 (400.0)" "2.0 - 5925.0 (578.0)"
[1] "hr=" "2.3"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED        13        3        11        4
  21Q LOSS WILD-TYPE     124       13        32        9
D68V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                 13                124
  STAGE II                 3                 13
  STAGE III               11                 32
  STAGE IV                 4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  21Q LOSS MUTATED    14   5    14
  21Q LOSS WILD-TYPE 132  17    37
D68V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                  14                132
  T2                   5                 17
  T3+T4               14                 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
  21Q LOSS MUTATED    6  4  1
  21Q LOSS WILD-TYPE 33 16  3
D68V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                6                 33
  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 15
  21Q LOSS WILD-TYPE 77  5 97
D68V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               11                 77
  M1                3                  5
  MX               15                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    15  18
  21Q LOSS WILD-TYPE  48 140
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     15   18
  21Q LOSS WILD-TYPE   48  140
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               15                 48
  MALE                 18                140
[1] 2 2
[1] FALSE
D68V8, continuous
D68V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  0     1
  21Q LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                           5    24
  21Q LOSS WILD-TYPE                        47   123
D68V10, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       5                 47
  WHITE                                          24                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"
D68V11, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     1  26
  21Q LOSS WILD-TYPE   8 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   26
  21Q LOSS WILD-TYPE    8  149
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               26                149
[1] 2 2
[1] FALSE

Clustering(69) Variable = 22Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    41   5
  22Q LOSS WILD-TYPE 146   2
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                46                148 
  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-B1-A47O TCGA-B3-3925 TCGA-B3-3926 TCGA-B9-A44B 
          26          223          513         1029          307           64 
TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5890 
         207         2639          270          792          921          233 
TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7055 
          29           84         3760         1864         1533          799 
TCGA-BQ-7056 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 
         612          218         2429          578           97           10 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC 
          36          208          765          446          786          262 
TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-MH-A856 TCGA-Q2-A5QZ TCGA-SX-A7SL 
         112           62            4          541          428          823 
TCGA-SX-A7SM TCGA-WN-AB4C TCGA-Y8-A896 TCGA-Y8-A8RZ 
        1973          882          186          205 

$`22Q LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207           21            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
          49            2          780          729          709           23 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ 
         600          436          379          516         1968            2 
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-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
        1357           67          595          659          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
         510           14          200          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
         309         1536          857          803          627           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W9 
          35          460         1338          671          585            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 
         452          167           52          586         1938         1454 
TCGA-BQ-5883 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
        1242          792          771          403          364         2948 
TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 
        2839         1516          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-6132 TCGA-DZ-6134 
         114          445           92         1240         2460         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6790 
        1670         1040          757            7           13         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
        1479         1194         1059          194          197         1967 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        1965         5925          393          841           32          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
         546           27          341          140         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         360         1726         2228          167          511          608 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
         677          649          146          376          364          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          845          924          841          616 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
          11          369          493          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
        2584         2816          391          540         1457         1443 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR 
        1005          876          578         1175         1266          805 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 
        1469         1331          579          224            2          219 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         181          399          106          104 

  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 
             367.5              583.5 
[1] "4.0 - 3760.0 (367.5)" "2.0 - 5925.0 (583.5)"
[1] "hr=" "8.9"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED        17        3        21        7
  22Q LOSS WILD-TYPE     120       13        22        6
D69V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                 17                120
  STAGE II                 3                 13
  STAGE III               21                 22
  STAGE IV                 7                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  22Q LOSS MUTATED    20   3    27
  22Q LOSS WILD-TYPE 126  19    24
D69V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                  20                126
  T2                   3                 19
  T3+T4               27                 24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  22Q LOSS MUTATED    9 12  2
  22Q LOSS WILD-TYPE 30  8  2
D69V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                9                 30
  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 23
  22Q LOSS WILD-TYPE 68  3 89
D69V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               20                 68
  M1                5                  3
  MX               23                 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"
D69V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    25  25
  22Q LOSS WILD-TYPE  38 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     25   25
  22Q LOSS WILD-TYPE   38  133
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               25                 38
  MALE                 25                133
[1] 2 2
[1] FALSE
D69V8, continuous
D69V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  0     3
  22Q LOSS WILD-TYPE                                2     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                          10    35
  22Q LOSS WILD-TYPE                        42   112
D69V10, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                  2
  BLACK OR AFRICAN AMERICAN                      10                 42
  WHITE                                          35                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"
D69V11, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     3  35
  22Q LOSS WILD-TYPE   6 140
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3   35
  22Q LOSS WILD-TYPE    6  140
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO               35                140
[1] 2 2
[1] FALSE

Clustering(70) Variable = XQ LOSS MUTATION ANALYSIS
D70V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    13   4
  XQ LOSS WILD-TYPE 174   3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               17               177 
  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-F9-A97G TCGA-G7-7501 TCGA-G7-A8LD TCGA-J7-8537 TCGA-Q2-A5QZ 
          13          446         1967            4          428 

$`XQ LOSS WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207          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-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
        1968            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-A47O TCGA-B1-A654 TCGA-B1-A655 
         595          659          747          513          108          510 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
          14          200         1029          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
         309         1536          857          803          627           14 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
          35         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 
           5          452          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-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-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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         194          197          262         1965         5925          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
         112          841           32          378          546           27 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         341          140         2072          408          360         1726 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        2228          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          376          364          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          845          924          841          616           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
        2584         2816          391          540         1457         1443 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1005          876          823         1973          578         1175 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C 
        1266          805         1469         1331          579          882 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
         224            2          186          219          181          399 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         205          106          104 

  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 
              307               579 
[1] "4.0 - 2429.0 (307.0)" "2.0 - 5925.0 (579.0)"
[1] "hr=" "15" 
D70V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED         5        1        11        3
  XQ LOSS WILD-TYPE     132       15        32       10
D70V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 5               132
  STAGE II                1                15
  STAGE III              11                32
  STAGE IV                3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  XQ LOSS MUTATED     6   1    14
  XQ LOSS WILD-TYPE 140  21    37
D70V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1                  6               140
  T2                  1                21
  T3+T4              14                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    3  7  1
  XQ LOSS WILD-TYPE 36 13  3
D70V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0               3                36
  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     8   2   9
  XQ LOSS WILD-TYPE  80   6 103
D70V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0               8                80
  M1               2                 6
  MX               9               103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    10  11
  XQ LOSS WILD-TYPE  53 147
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     10   11
  XQ LOSS WILD-TYPE   53  147
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              10                53
  MALE                11               147
[1] 2 2
[1] FALSE
D70V8, continuous
D70V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0     3
  XQ LOSS WILD-TYPE                                2     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           6    11
  XQ LOSS WILD-TYPE                        46   136
D70V10, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                 2
  BLACK OR AFRICAN AMERICAN                      6                46
  WHITE                                         11               136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V11, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0  15
  XQ LOSS WILD-TYPE   9 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   15
  XQ LOSS WILD-TYPE    9  160
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              15               160
[1] 2 2
[1] FALSE
