[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"        "-oTESCA-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/ESCA-TP/11541396/ESCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/11548801/transformed.cor.cli.txt"

nPatients in clinical file=151, in cluster file=184, common to both=150
[1]  80 150
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               26               124 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               26               124 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               47               103 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               47               103 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               47               103 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               47               103 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               35               115 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               35               115 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               22               128 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               22               128 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               63                87 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               63                87 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12               138 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12               138 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               13               137 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               13               137 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               60                90 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               60                90 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               18               132 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               18               132 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               34               116 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               34               116 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               28               122 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               28               122 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               90                60 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               90                60 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               72                78 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               72                78 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               56                94 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               56                94 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               81                69 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               81                69 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               12               138 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               12               138 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               23               127 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               23               127 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                31                119 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                31                119 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                24                126 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                24                126 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                33                117 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                33                117 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                25                125 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                25                125 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                46                104 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                46                104 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                30                120 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                30                120 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                37                113 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                37                113 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                38                112 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                38                112 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                24                126 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                24                126 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                32                118 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                32                118 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                28                122 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                28                122 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                24                126 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                24                126 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                36                114 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                36                114 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                41                109 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                41                109 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                22                128 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                22                128 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                21                129 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                21                129 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                31                119 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                31                119 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                88                 62 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                88                 62 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                97                 53 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                97                 53 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                14                136 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                14                136 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                127 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                127 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               28               122 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               28               122 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               31               119 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               31               119 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               17               133 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               17               133 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                8               142 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                8               142 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               15               135 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               15               135 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               74                76 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               74                76 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               23               127 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               23               127 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               85                65 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               85                65 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               74                76 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               74                76 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               38               112 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               38               112 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               67                83 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               67                83 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               29               121 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               29               121 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               30               120 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               30               120 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               12               138 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               12               138 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               19               131 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               19               131 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               52                98 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               52                98 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               20               130 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               20               130 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               82                68 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               82                68 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               51                99 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               51                99 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                35                115 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                35                115 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                37                113 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                37                113 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                39                111 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                39                111 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                43                107 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                43                107 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                30                120 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                30                120 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                25                125 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                25                125 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                53                 97 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                53                 97 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                39                111 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                39                111 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                45                105 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                45                105 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                45                105 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                45                105 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                44                106 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                44                106 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                58                 92 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                58                 92 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                17                133 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                17                133 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                62                 88 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                62                 88 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                84                 66 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                84                 66 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                54                 96 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                54                 96 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                41                109 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                41                109 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                17                133 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                17                133 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                144 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                144 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                85                 65 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                85                 65 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                64                 86 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                64                 86 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               37               113 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               37               113 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "NUMBERPACKYEARSSMOKED"                 
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCHNUMBER"                           

Input Data has 15 rows and 150 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
          NA           NA           NA           NA           NA           NA 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
          NA           NA           NA           NA           NA         1012 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
         611           NA          632           80          612            1 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
           8           30           16          518           NA          712 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
          11            4          452           14           13           NA 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        3714           NA         1837         2069           NA           NA 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        1301          773          471          705          769          550 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
         535          189           96          105           NA           NA 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
         272          107          112          102          593          267 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
         195          124           NA          101          218           NA 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
          NA          935           NA          882           NA           NA 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
         211          265           79           NA           11          225 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
         120           92         1688           NA         1094           NA 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
          NA          501          412          402           NA          165 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
          NA          265          408          825           NA           NA 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
          NA          315            2          318            5            2 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
          10           NA            3            4            2            3 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
           2            3            2           NA            4            2 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
           3            3            3            2            2            3 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
           2            6           36           NA           NA           NA 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
          NA           NA          536           NA          115           NA 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
          NA           NA          447           NA          900           NA 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        1641           NA           NA          267          426           NA 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU 
          NA          146          258          248          135           NA 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
          NA         1117          366           NA           NA          551 
Variable 1:'AGE':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=78,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'NUMBERPACKYEARSSMOKED':	nDistinctValues=38,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "PATHOLOGY.M.STAGE"     "GENDER"               
[7] "NUMBERPACKYEARSSMOKED" "RACE"                 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 150 columns, 1 survival variables, and 8 non-survival variables.
AGE, nv=46, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
 1 25 33 74  4 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   26    33    74     4 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T0 T1 T2 T3 T4 
 1 25 33 74  4 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   26    33    74     4 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
64 54 11  6 
[1] "table(vv)"
vv
N0 N1 N2 N3 
64 54 11  6 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 N3 
64 54 11  6 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
64 54 11  6 
PATHOLOGY.M.STAGE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=38, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED   18  8
  1P GAIN WILD-TYPE 70 46
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               26               116 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8                46 
$`1P GAIN MUTATED`
TCGA-2H-A9GM TCGA-IG-A3QL TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-JY-A93E 
       13.94        20.09        17.03        23.41         0.46        18.08 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OX TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
        4.08        18.35         7.43         0.36         3.95         3.02 
TCGA-L5-A8NF TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        2.66        13.22        13.41        10.36         0.07        10.45 
TCGA-LN-A49X TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-V5-A7RC 
        0.10         0.07         0.20        14.70        29.59         3.42 
TCGA-VR-A8EW TCGA-ZR-A9CJ 
        8.12        18.12 

$`1P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 
        8.94        16.24         4.21        32.45        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12         0.03         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
        0.53         0.79         0.36         0.13        14.86         0.43 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
      122.10        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       42.77        25.41        15.48        23.18        25.28        17.59 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
        6.21         3.16         3.45         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.52         3.68         3.35        19.50         8.78         6.41 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        30.74         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         6.94         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        7.40        55.50        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT 
       13.55         7.76         5.42        21.37         8.71        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       83.24        52.57        46.09         0.16         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y 
        0.10         0.13         0.07         0.10         0.07         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.13         0.07         0.10         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.07         0.10         1.18        17.62         5.16         3.78 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        8.02         7.59         5.06         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        9.30         7.00         8.78        14.01         5.29         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.48         8.15         4.44        18.31        36.72        12.03 
TCGA-VR-AA7D TCGA-VR-AA7I 
        9.17        15.91 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.07              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            29.59            122.10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            9.240             7.285 
[1] "0.1 - 29.6 (9.2)"  "0.0 - 122.1 (7.3)"
[1] "hr=" "1"  
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED         1        1        0        0         4         8
  1P GAIN WILD-TYPE       7        3        6        1        31        18
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED           1          1          2          2        0
  1P GAIN WILD-TYPE        22         10          6          4        3
                   vv
clus                STAGE IVA
  1P GAIN MUTATED           1
  1P GAIN WILD-TYPE         1
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 1                 3
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                4                31
  STAGE IIB                8                18
  STAGE III                1                22
  STAGE IIIA               1                10
  STAGE IIIB               2                 6
  STAGE IIIC               2                 4
  STAGE IV                 0                 3
  STAGE IVA                1                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  1P GAIN MUTATED       7  4 12  0
  1P GAIN WILD-TYPE    19 29 62  4
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1               7                19
  T2                  4                29
  T3                 12                62
  T4                  0                 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                N0 N1 N2 N3
  1P GAIN MUTATED   11  8  2  2
  1P GAIN WILD-TYPE 53 46  9  4
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              11                53
  N1               8                46
  N2               2                 9
  N3               2                 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                M0 M1 M1A MX
  1P GAIN MUTATED   17  0   1  3
  1P GAIN WILD-TYPE 94  2   2 14
D1V6, multiclass
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               17                94
  M1                0                 2
  M1A               1                 2
  MX                3                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     3  23
  1P GAIN WILD-TYPE  18 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3   23
  1P GAIN WILD-TYPE   18  106
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               3                18
  MALE                23               106
[1] 2 2
[1] FALSE
D1V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       7                         1    17
  1P GAIN WILD-TYPE    31                         1    76
D1V9, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   7                31
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  17                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   29 16
  1Q GAIN WILD-TYPE 59 38
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               45                97 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               16                38 
$`1Q GAIN MUTATED`
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 
       13.94         8.94        20.09         0.85        20.12         0.03 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A93D 
       17.03         0.79        23.41         0.36         0.46        25.28 
TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
       18.08         0.30         3.68        19.50         4.08        18.35 
TCGA-L5-A4OX TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        7.43         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L7-A6VZ 
        2.66        12.92        13.22         5.42        13.41        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 
        0.07        10.45         0.07         0.10         0.10         0.13 
TCGA-LN-A4A3 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-V5-A7RC 
        0.07         0.07         0.20        14.70        29.59         3.42 
TCGA-VR-A8EW TCGA-VR-AA7I TCGA-ZR-A9CJ 
        8.12        15.91        18.12 

$`1Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A3YB 
       16.24         4.21        32.45        33.27        20.78         2.63 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
        0.26         0.99         0.53         0.13        14.86         0.43 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
      122.10        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC 
       42.77        25.41        15.48        23.18        17.59         6.21 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
        3.16         3.45         4.31         8.94         3.52         3.35 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
        8.78         6.41         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T 
       30.74         4.90        29.00         7.13         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        2.60        25.12        35.97        13.48        16.47        13.55 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76        21.37         8.71        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       46.09         0.16         0.07         0.33         0.10         0.13 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.07         0.07         0.10         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.07         0.10         1.18        17.62         5.16         3.78 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        8.02         7.59         5.06         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        9.30         7.00         8.78        14.01         5.29         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.48         8.15         4.44        18.31        36.72        12.03 
TCGA-VR-AA7D 
        9.17 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.03              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             55.5             122.1 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             7.40              7.63 
[1] "0.0 - 55.5 (7.4)"  "0.1 - 122.1 (7.6)"
[1] "hr=" "1.3"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED         2        1        1        0        10        11
  1Q GAIN WILD-TYPE       6        3        5        1        25        15
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           6          3          3          3        1
  1Q GAIN WILD-TYPE        17          8          5          3        2
                   vv
clus                STAGE IVA
  1Q GAIN MUTATED           1
  1Q GAIN WILD-TYPE         1
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 1                 3
  STAGE IB                 1                 5
  STAGE II                 0                 1
  STAGE IIA               10                25
  STAGE IIB               11                15
  STAGE III                6                17
  STAGE IIIA               3                 8
  STAGE IIIB               3                 5
  STAGE IIIC               3                 3
  STAGE IV                 1                 2
  STAGE IVA                1                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  1Q GAIN MUTATED      11  9 22  2
  1Q GAIN WILD-TYPE    15 24 52  2
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1              11                15
  T2                  9                24
  T3                 22                52
  T4                  2                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  1Q GAIN MUTATED   21 17  3  3
  1Q GAIN WILD-TYPE 43 37  8  3
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              21                43
  N1              17                37
  N2               3                 8
  N3               3                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  1Q GAIN MUTATED   36  1   1  3
  1Q GAIN WILD-TYPE 75  1   2 14
D2V6, multiclass
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0               36                75
  M1                1                 1
  M1A               1                 2
  MX                3                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    4 43
  1Q GAIN WILD-TYPE 17 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      4   43
  1Q GAIN WILD-TYPE   17   86
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               4                17
  MALE                43                86
[1] 2 2
[1] FALSE
D2V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED      14                         1    30
  1Q GAIN WILD-TYPE    24                         1    63
D2V9, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                  14                24
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  30                63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED   26 19
  2P GAIN WILD-TYPE 62 35
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               45                97 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               19                35 
$`2P GAIN MUTATED`
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A4P3 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-JY-A6FA 
       13.94         8.94         0.03        23.41         0.46        44.75 
TCGA-JY-A93E TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
       18.08         4.31         3.68        19.50         4.08        18.35 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NV 
        3.32         3.16         7.13         2.60         0.36        52.57 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49Y 
       10.36         0.07        10.45         0.10         0.13         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U6 
        0.13         0.07         0.10         0.10         0.10         0.20 
TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        1.18         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
       29.59         6.35        53.95        14.01         3.42         4.80 
TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-A8EW 
        8.48        18.31         8.12 

$`2P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12         0.26         0.99         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
       17.03         0.79         0.36         0.13        14.86         0.43 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       25.41        15.48        23.18        25.28        17.59         6.21 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
        3.16         3.45         0.30         8.94         3.52         3.35 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
        8.78         6.41         7.17         1.38        30.74         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.43         6.94         8.71        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.42 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW 
       21.37         8.71        13.41        27.12        83.24        46.09 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
        0.16         0.07         0.33         0.07         0.10         0.07 
TCGA-LN-A49X TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-M9-A5M8 
        0.10         0.10         0.07         0.07         0.07        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        5.16         3.78         9.30         7.00         8.78         5.29 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        8.15         4.44        36.72        12.03         9.17        15.91 
TCGA-ZR-A9CJ 
       18.12 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.03              0.07 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            53.95            122.10 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             5.06              8.71 
[1] "0.0 - 54.0 (5.1)"  "0.1 - 122.1 (8.7)"
[1] "hr=" "1.7"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         1        2        2        1         9        10
  2P GAIN WILD-TYPE       7        2        4        0        26        16
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED           6          1          2          2        1
  2P GAIN WILD-TYPE        17         10          6          4        2
                   vv
clus                STAGE IVA
  2P GAIN MUTATED           0
  2P GAIN WILD-TYPE         2
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 2                 2
  STAGE IB                 2                 4
  STAGE II                 1                 0
  STAGE IIA                9                26
  STAGE IIB               10                16
  STAGE III                6                17
  STAGE IIIA               1                10
  STAGE IIIB               2                 6
  STAGE IIIC               2                 4
  STAGE IV                 1                 2
  STAGE IVA                0                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  2P GAIN MUTATED       9  9 20  0
  2P GAIN WILD-TYPE    17 24 54  4
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1               9                17
  T2                  9                24
  T3                 20                54
  T4                  0                 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                N0 N1 N2 N3
  2P GAIN MUTATED   19 15  2  2
  2P GAIN WILD-TYPE 45 39  9  4
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              19                45
  N1              15                39
  N2               2                 9
  N3               2                 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                M0 M1 M1A MX
  2P GAIN MUTATED   27  1   0  7
  2P GAIN WILD-TYPE 84  1   3 10
D3V6, multiclass
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0               27                84
  M1                1                 1
  M1A               0                 3
  MX                7                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"
D3V7, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    4 43
  2P GAIN WILD-TYPE 17 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      4   43
  2P GAIN WILD-TYPE   17   86
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               4                17
  MALE                43                86
[1] 2 2
[1] FALSE
D3V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED      17                         2    25
  2P GAIN WILD-TYPE    21                         0    68
D3V9, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                  17                21
  BLACK OR AFRICAN AMERICAN               2                 0
  WHITE                                  25                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED   19 14
  2Q GAIN WILD-TYPE 69 40
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               33               109 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               14                40 
$`2Q GAIN MUTATED`
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A5S3 TCGA-JY-A6FA TCGA-JY-A93E TCGA-L5-A43J 
       13.94         8.94        23.41        44.75        18.08         4.31 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y 
        3.68        19.50         3.32         7.13         2.60         0.36 
TCGA-L5-A8NE TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A4A2 TCGA-LN-A4A4 
       55.50        52.57         0.07         0.10         0.13         0.10 
TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.10         0.20         1.18         3.78         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-V5-A7RC 
        5.06        14.70        29.59         6.35        53.95         3.42 
TCGA-V5-A7RE TCGA-VR-A8EU TCGA-VR-A8EW 
        4.80        18.31         8.12 

$`2Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12         0.03         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03         0.79         0.36         0.13        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        0.46         0.43       122.10        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        15.48        23.18        25.28 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M 
       17.59         6.21         3.16         3.45         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.52         3.35         8.78         6.41         4.08        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        30.74         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43         6.94         8.71        25.12         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.42        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L 
       13.41        27.12        83.24        46.09        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
        0.16         0.07         0.33         0.13         0.07         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.07         0.10         0.07         0.07         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6L6 
        0.07         0.10         0.07        17.62         5.16         7.04 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV 
        9.30         7.00         8.78        14.01         5.29         8.48 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        8.15         4.44        36.72        12.03         9.17        15.91 
TCGA-ZR-A9CJ 
       18.12 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.07              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             55.5             122.1 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             6.35              7.76 
[1] "0.1 - 55.5 (6.3)"  "0.0 - 122.1 (7.8)"
[1] "hr=" "1.2"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q GAIN MUTATED         1        0        1        1         6         8
  2Q GAIN WILD-TYPE       7        4        5        0        29        18
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           4          1          2          1        1
  2Q GAIN WILD-TYPE        19         10          6          5        2
                   vv
clus                STAGE IVA
  2Q GAIN MUTATED           0
  2Q GAIN WILD-TYPE         2
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 4
  STAGE IB                 1                 5
  STAGE II                 1                 0
  STAGE IIA                6                29
  STAGE IIB                8                18
  STAGE III                4                19
  STAGE IIIA               1                10
  STAGE IIIB               2                 6
  STAGE IIIC               1                 5
  STAGE IV                 1                 2
  STAGE IVA                0                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  2Q GAIN MUTATED       6  7 14  0
  2Q GAIN WILD-TYPE    20 26 60  4
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1               6                20
  T2                  7                26
  T3                 14                60
  T4                  0                 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                N0 N1 N2 N3
  2Q GAIN MUTATED   12 12  2  1
  2Q GAIN WILD-TYPE 52 42  9  5
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              12                52
  N1              12                42
  N2               2                 9
  N3               1                 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                M0 M1 M1A MX
  2Q GAIN MUTATED   22  1   0  3
  2Q GAIN WILD-TYPE 89  1   3 14
D4V6, multiclass
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0               22                89
  M1                1                 1
  M1A               0                 3
  MX                3                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    3 32
  2Q GAIN WILD-TYPE 18 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3   32
  2Q GAIN WILD-TYPE   18   97
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               3                18
  MALE                32                97
[1] 2 2
[1] FALSE
D4V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED      11                         1    20
  2Q GAIN WILD-TYPE    27                         1    73
D4V9, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                  11                27
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  20                73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED   11 10
  3P GAIN WILD-TYPE 77 44
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               21               121 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                44 
$`3P GAIN MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GO TCGA-IG-A4P3 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43H 
       31.27        16.24         0.03        23.18        18.08         0.30 
TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NT 
        4.31         4.08         3.16         3.95        55.50        27.12 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R TCGA-Q9-A6FU TCGA-R6-A6KZ 
       52.57        10.36        10.45         0.10         5.16         5.06 
TCGA-R6-A6Y0 TCGA-V5-AASW TCGA-ZR-A9CJ 
       53.95         8.15        18.12 

$`3P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94         4.21        32.45        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12         0.26         0.99         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41         0.36         0.13        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.46         0.43       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D 
        3.68        41.52        42.77        25.41        15.48        25.28 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OE 
       17.59         6.21         3.16         3.45         8.94         3.52 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
        3.68         3.35        19.50         8.78         6.41        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        0.36         7.40         3.02         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.42 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49K 
       21.37         8.71        13.41        83.24        46.09         0.07 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
        0.16         0.07         0.33         0.13         0.07         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.07         0.10         0.07         0.13         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.10         0.10         0.07         0.07         0.10         0.07 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.20         1.18        17.62         3.78         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO 
       14.70         7.04        29.59         6.35         9.30         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        8.78        14.01         5.29         3.42         4.80         8.48 
TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
        4.44        18.31         8.12        36.72        12.03         9.17 
TCGA-VR-AA7I 
       15.91 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.03              0.07 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             55.5             122.1 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            10.36              7.40 
[1] "0.0 - 55.5 (10.4)" "0.1 - 122.1 (7.4)"
[1] "hr=" "1.1"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED         0        2        0        0         3         5
  3P GAIN WILD-TYPE       8        2        6        1        32        21
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED           2          1          2          2        0
  3P GAIN WILD-TYPE        21         10          6          4        3
                   vv
clus                STAGE IVA
  3P GAIN MUTATED           1
  3P GAIN WILD-TYPE         1
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 2                 2
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                3                32
  STAGE IIB                5                21
  STAGE III                2                21
  STAGE IIIA               1                10
  STAGE IIIB               2                 6
  STAGE IIIC               2                 4
  STAGE IV                 0                 3
  STAGE IVA                1                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  3P GAIN MUTATED       3  3 13  0
  3P GAIN WILD-TYPE    23 30 61  4
D5V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1               3                23
  T2                  3                30
  T3                 13                61
  T4                  0                 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                N0 N1 N2 N3
  3P GAIN MUTATED    7  8  2  2
  3P GAIN WILD-TYPE 57 46  9  4
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0               7                57
  N1               8                46
  N2               2                 9
  N3               2                 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                M0 M1 M1A MX
  3P GAIN MUTATED   13  0   1  4
  3P GAIN WILD-TYPE 98  2   2 13
D5V6, multiclass
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               13                98
  M1                0                 2
  M1A               1                 2
  MX                4                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"
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     2  20
  3P GAIN WILD-TYPE  19 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   20
  3P GAIN WILD-TYPE   19  109
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               2                19
  MALE                20               109
[1] 2 2
[1] FALSE
D5V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       4                         0    16
  3P GAIN WILD-TYPE    34                         2    77
D5V9, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   4                34
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  16                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED   39 22
  3Q GAIN WILD-TYPE 49 32
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               61                81 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               22                32 
$`3Q GAIN MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IG-A3I8 TCGA-IG-A3QL 
       31.27        58.55         7.63        16.24        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        0.85         2.63         0.03         0.26         0.53        17.03 
TCGA-IG-A97H TCGA-JY-A6FB TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43J 
        0.43        60.39        23.18        18.08         0.30         4.31 
TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 
        4.08         3.16         7.13         6.94         2.60         3.95 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR 
       55.50         2.66        35.97        16.47        13.22         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N 
       13.41        27.12        52.57        10.36        10.45         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.33         0.10         0.13         0.10         0.13         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-Q9-A6FU 
        0.10         0.10         0.07         0.07         0.10         5.16 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-A7RC 
        8.02         7.59         5.06        53.95        14.01         3.42 
TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
        8.15        18.31         8.12        36.72        12.03         9.17 
TCGA-ZR-A9CJ 
       18.12 

$`3Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       25.78        14.30         5.92        13.94         8.94         4.21 
TCGA-2H-A9GR TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 
       32.45        20.78        20.12         0.99         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA 
        0.36         0.13        14.86         0.46       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        15.48 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M 
       25.28        17.59         6.21         3.16         3.45         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.52         3.68         3.35        19.50         8.78         6.41 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        30.74         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
       29.00         7.43         8.71        25.12         0.36         7.40 
TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
        3.02        12.92        13.48        13.55         7.76         5.42 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49U 
       21.37        83.24        46.09         0.07         0.16         0.07 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-LN-A5U6 
        0.07         0.10         0.07         0.10         0.07         0.20 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        1.18        17.62         3.78        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        6.35         9.30         7.00         8.78         5.29         4.80 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-AA7I 
        8.48         4.44        15.91 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.03              0.07 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            60.39            122.10 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             7.59              7.43 
[1] "0.0 - 60.4 (7.6)"  "0.1 - 122.1 (7.4)"
[1] "hr=" "1"  
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED         2        2        2        0        13        10
  3Q GAIN WILD-TYPE       6        2        4        1        22        16
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED          11          6          4          3        1
  3Q GAIN WILD-TYPE        12          5          4          3        2
                   vv
clus                STAGE IVA
  3Q GAIN MUTATED           2
  3Q GAIN WILD-TYPE         0
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 2                 2
  STAGE IB                 2                 4
  STAGE II                 0                 1
  STAGE IIA               13                22
  STAGE IIB               10                16
  STAGE III               11                12
  STAGE IIIA               6                 5
  STAGE IIIB               4                 4
  STAGE IIIC               3                 3
  STAGE IV                 1                 2
  STAGE IVA                2                 0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  3Q GAIN MUTATED       8 11 37  1
  3Q GAIN WILD-TYPE    18 22 37  3
D6V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1               8                18
  T2                 11                22
  T3                 37                37
  T4                  1                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  3Q GAIN MUTATED   24 24  5  3
  3Q GAIN WILD-TYPE 40 30  6  3
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              24                40
  N1              24                30
  N2               5                 6
  N3               3                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  3Q GAIN MUTATED   46  1   2  7
  3Q GAIN WILD-TYPE 65  1   1 10
D6V6, multiclass
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0               46                65
  M1                1                 1
  M1A               2                 1
  MX                7                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"
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    7 56
  3Q GAIN WILD-TYPE 14 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      7   56
  3Q GAIN WILD-TYPE   14   73
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               7                14
  MALE                56                73
[1] 2 2
[1] FALSE
D6V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED      19                         1    36
  3Q GAIN WILD-TYPE    19                         1    57
D6V9, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                  19                19
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  36                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED    7  4
  4P GAIN WILD-TYPE 81 50
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               11               131 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4                50 
$`4P GAIN MUTATED`
TCGA-IG-A3YB TCGA-IG-A5S3 TCGA-JY-A6F8 TCGA-L5-A43J TCGA-L5-A4ON TCGA-L5-A8NE 
        2.63        23.41       122.10         4.31        18.35        55.50 
TCGA-L5-A8NV TCGA-LN-A4A9 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       52.57         0.07        29.59        53.95         9.30 

$`4P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       20.09         0.85        20.78        20.12         0.03         0.26 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        0.99         0.53        17.03         0.79         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86         0.46         0.43        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.68        41.52        42.77        25.41        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       25.28        18.08        17.59         6.21         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         8.94         3.52         3.68         3.35        19.50 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
        8.78         6.41         4.08         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        30.74         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        6.94         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.95         3.02         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.42        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        13.41        27.12        83.24        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
        0.07        10.45         0.16         0.07         0.33         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.13         0.07         0.10         0.07         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.13         0.07         0.10         0.10         0.10         0.07 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.10         0.07         0.20         1.18        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        3.78         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XQ TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        6.35         7.00         8.78        14.01         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW 
        4.80         8.48         8.15         4.44        18.31         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
       36.72        12.03         9.17        15.91        18.12 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.07              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           122.10             83.24 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            23.41              7.17 
[1] "0.1 - 122.1 (23.4)" "0.0 - 83.2 (7.2)"  
[1] "hr=" "2.4"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         1        0        0        0         2         4
  4P GAIN WILD-TYPE       7        4        6        1        33        22
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED           1          1          0          0        0
  4P GAIN WILD-TYPE        22         10          8          6        3
                   vv
clus                STAGE IVA
  4P GAIN MUTATED           0
  4P GAIN WILD-TYPE         2
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 4
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                2                33
  STAGE IIB                4                22
  STAGE III                1                22
  STAGE IIIA               1                10
  STAGE IIIB               0                 8
  STAGE IIIC               0                 6
  STAGE IV                 0                 3
  STAGE IVA                0                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  4P GAIN MUTATED       2  2  5  0
  4P GAIN WILD-TYPE    24 31 69  4
D7V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1               2                24
  T2                  2                31
  T3                  5                69
  T4                  0                 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                N0 N1 N2 N3
  4P GAIN MUTATED    5  4  0  0
  4P GAIN WILD-TYPE 59 50 11  6
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               5                59
  N1               4                50
  N2               0                11
  N3               0                 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                 M0  M1 M1A  MX
  4P GAIN MUTATED     7   0   0   1
  4P GAIN WILD-TYPE 104   2   3  16
D7V6, multiclass
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0                7               104
  M1                0                 2
  M1A               0                 3
  MX                1                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  11
  4P GAIN WILD-TYPE  20 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   11
  4P GAIN WILD-TYPE   20  118
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               1                20
  MALE                11               118
[1] 2 2
[1] FALSE
D7V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       2                         0    10
  4P GAIN WILD-TYPE    36                         2    83
D7V9, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   2                36
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  10                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED    7  5
  4Q GAIN WILD-TYPE 81 49
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               12               130 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5                49 
$`4Q GAIN MUTATED`
TCGA-IG-A3YA TCGA-IG-A5S3 TCGA-JY-A6F8 TCGA-L5-A43H TCGA-L5-A4ON TCGA-L5-A8NE 
       20.78        23.41       122.10         0.30        18.35        55.50 
TCGA-L5-A8NV TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-R6-A6Y0 TCGA-V5-A7RC TCGA-VR-A8EW 
       52.57         0.07         0.07        53.95         3.42         8.12 

$`4Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       20.09         0.85         2.63        20.12         0.03         0.26 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        0.99         0.53        17.03         0.79         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86         0.46         0.43        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.68        41.52        42.77        25.41        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       25.28        18.08        17.59         6.21         3.16         3.45 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        4.31         8.94         3.52         3.68         3.35        19.50 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
        8.78         6.41         4.08         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        30.74         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        6.94         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.95         3.02         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.42        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        13.41        27.12        83.24        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
        0.07        10.45         0.16         0.07         0.33         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.13         0.07         0.10         0.07         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ 
        0.13         0.07         0.10         0.10         0.10         0.10 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.07         0.20         1.18        17.62         5.16         3.78 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        6.35         9.30         7.00         8.78        14.01         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8Q7 
        4.80         8.48         8.15         4.44        18.31        36.72 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
       12.03         9.17        15.91        18.12 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.07              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           122.10             83.24 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           19.565             7.285 
[1] "0.1 - 122.1 (19.6)" "0.0 - 83.2 (7.3)"  
[1] "hr=" "1.8"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q GAIN MUTATED         1        0        0        0         3         3
  4Q GAIN WILD-TYPE       7        4        6        1        32        23
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED           2          1          1          0        0
  4Q GAIN WILD-TYPE        21         10          7          6        3
                   vv
clus                STAGE IVA
  4Q GAIN MUTATED           0
  4Q GAIN WILD-TYPE         2
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 4
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                3                32
  STAGE IIB                3                23
  STAGE III                2                21
  STAGE IIIA               1                10
  STAGE IIIB               1                 7
  STAGE IIIC               0                 6
  STAGE IV                 0                 3
  STAGE IVA                0                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  4Q GAIN MUTATED       2  3  5  1
  4Q GAIN WILD-TYPE    24 30 69  3
D8V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1               2                24
  T2                  3                30
  T3                  5                69
  T4                  1                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  4Q GAIN MUTATED    6  4  1  0
  4Q GAIN WILD-TYPE 58 50 10  6
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               6                58
  N1               4                50
  N2               1                10
  N3               0                 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                 M0  M1 M1A  MX
  4Q GAIN MUTATED    10   0   0   0
  4Q GAIN WILD-TYPE 101   2   3  17
D8V6, multiclass
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               10               101
  M1                0                 2
  M1A               0                 3
  MX                0                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  12
  4Q GAIN WILD-TYPE  20 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   12
  4Q GAIN WILD-TYPE   20  117
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               1                20
  MALE                12               117
[1] 2 2
[1] FALSE
D8V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       4                         1     8
  4Q GAIN WILD-TYPE    34                         1    85
D8V9, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   4                34
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                   8                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   37 19
  5P GAIN WILD-TYPE 51 35
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               56                86 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               19                35 
$`5P GAIN MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC 
       14.30         5.92        32.45        33.27         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD 
        0.03         0.79        23.41         0.43        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43J 
        3.68        42.77        25.28        18.08         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
        8.94        19.50         8.78         4.08         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88Y 
        3.16         4.90        29.00         7.13         6.94         0.36 
TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NV TCGA-L7-A6VZ 
       55.50        35.97        12.92        13.55        52.57        10.36 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A6 
        0.33         0.10         0.07         0.07         0.10         0.10 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.10         0.07         0.20         5.16         5.06        14.70 
TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8Q7 TCGA-VR-AA4G 
       53.95         7.00        14.01         3.42        36.72        12.03 
TCGA-VR-AA7I TCGA-ZR-A9CJ 
       15.91        18.12 

$`5P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS 
       16.24         4.21        20.09         0.85        20.78         0.26 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.99         0.53        17.03         0.36         0.13        14.86 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 
        0.46       122.10        60.39        41.52        25.41        15.48 
TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OE 
       23.18        17.59         6.21         3.16         3.45         3.52 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS 
        3.68         3.35         6.41        18.35         1.38        30.74 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43         8.71         2.60        25.12         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        3.02         2.66        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        5.42        21.37         8.71        13.41        27.12        83.24 
TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S 
       46.09         0.07        10.45         0.16         0.07         0.13 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
        0.07         0.10         0.10         0.13         0.07         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.07         0.07         1.18        17.62         3.78         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-S8-A6BV 
        7.59         7.04        29.59         6.35         9.30         8.78 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU 
        5.29         4.80         8.48         8.15         4.44        18.31 
TCGA-VR-A8EW TCGA-VR-AA7D 
        8.12         9.17 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.03              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            68.02            122.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             7.15              7.61 
[1] "0.0 - 68.0 (7.2)"  "0.1 - 122.1 (7.6)"
[1] "hr=" "1.3"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED         1        3        3        1        14         9
  5P GAIN WILD-TYPE       7        1        3        0        21        17
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED          10          5          1          5        2
  5P GAIN WILD-TYPE        13          6          7          1        1
                   vv
clus                STAGE IVA
  5P GAIN MUTATED           0
  5P GAIN WILD-TYPE         2
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 3                 1
  STAGE IB                 3                 3
  STAGE II                 1                 0
  STAGE IIA               14                21
  STAGE IIB                9                17
  STAGE III               10                13
  STAGE IIIA               5                 6
  STAGE IIIB               1                 7
  STAGE IIIC               5                 1
  STAGE IV                 2                 1
  STAGE IVA                0                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  5P GAIN MUTATED       7 14 34  1
  5P GAIN WILD-TYPE    19 19 40  3
D9V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1               7                19
  T2                 14                19
  T3                 34                40
  T4                  1                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  5P GAIN MUTATED   26 21  3  5
  5P GAIN WILD-TYPE 38 33  8  1
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              26                38
  N1              21                33
  N2               3                 8
  N3               5                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  5P GAIN MUTATED   43  1   1 10
  5P GAIN WILD-TYPE 68  1   2  7
D9V6, multiclass
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0               43                68
  M1                1                 1
  M1A               1                 2
  MX               10                 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"
D9V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   11 49
  5P GAIN WILD-TYPE 10 80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     11   49
  5P GAIN WILD-TYPE   10   80
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              11                10
  MALE                49                80
[1] 2 2
[1] FALSE
D9V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED      16                         1    38
  5P GAIN WILD-TYPE    22                         1    55
D9V9, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                  16                22
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  38                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED   11  4
  5Q GAIN WILD-TYPE 77 50
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               15               127 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                4                50 
$`5Q GAIN MUTATED`
TCGA-IG-A3I8 TCGA-JY-A93E TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OO 
       33.27        18.08         8.94        19.50         8.78         3.32 
TCGA-L5-A88S TCGA-L7-A6VZ TCGA-LN-A49Y TCGA-LN-A4MR TCGA-R6-A6KZ TCGA-R6-A6L4 
        6.94        10.36         0.07         0.07         5.06        14.70 
TCGA-RE-A7BO TCGA-V5-A7RC TCGA-VR-AA7I 
        7.00         3.42        15.91 

$`5Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL 
       13.94         8.94        16.24         4.21        32.45        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12         0.03         0.26 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        0.99         0.53        17.03         0.79        23.41         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA 
        0.13        14.86         0.46         0.43       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       15.48        23.18        25.28        17.59         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.45         0.30         4.31         3.52         3.68         3.35 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
        6.41         4.08        18.35         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
       30.74         4.90        29.00         7.13         7.43         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        2.60        25.12         0.36         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
       55.50         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.42        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K 
       13.41        27.12        83.24        52.57        46.09         0.07 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45         0.16         0.07         0.33         0.10         0.13 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.07         0.10         0.07         0.10         0.13         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10         0.10         0.10         0.07         0.07         0.10 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.20         1.18        17.62         5.16         3.78         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59         7.04        29.59         6.35        53.95         9.30 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        8.78        14.01         5.29         4.80         8.48         8.15 
TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
        4.44        18.31         8.12        36.72        12.03         9.17 
TCGA-ZR-A9CJ 
       18.12 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.07              0.03 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            33.27            122.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             8.78              7.43 
[1] "0.1 - 33.3 (8.8)"  "0.0 - 122.1 (7.4)"
[1] "hr=" "1.3"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED         1        0        1        0         6         1
  5Q GAIN WILD-TYPE       7        4        5        1        29        25
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED           1          1          0          3        0
  5Q GAIN WILD-TYPE        22         10          8          3        3
                   vv
clus                STAGE IVA
  5Q GAIN MUTATED           0
  5Q GAIN WILD-TYPE         2
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 4
  STAGE IB                 1                 5
  STAGE II                 0                 1
  STAGE IIA                6                29
  STAGE IIB                1                25
  STAGE III                1                22
  STAGE IIIA               1                10
  STAGE IIIB               0                 8
  STAGE IIIC               3                 3
  STAGE IV                 0                 3
  STAGE IVA                0                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  5Q GAIN MUTATED       2  3  9  1
  5Q GAIN WILD-TYPE    24 30 65  3
D10V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1               2                24
  T2                  3                30
  T3                  9                65
  T4                  1                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  5Q GAIN MUTATED    9  2  1  3
  5Q GAIN WILD-TYPE 55 52 10  3
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0               9                55
  N1               2                52
  N2               1                10
  N3               3                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  5Q GAIN MUTATED    11   0   0   4
  5Q GAIN WILD-TYPE 100   2   3  13
D10V6, multiclass
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               11               100
  M1                0                 2
  M1A               0                 3
  MX                4                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"
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     3  15
  5Q GAIN WILD-TYPE  18 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3   15
  5Q GAIN WILD-TYPE   18  114
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               3                18
  MALE                15               114
[1] 2 2
[1] FALSE
D10V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       5                         1    11
  5Q GAIN WILD-TYPE    33                         1    82
D10V9, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   5                33
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  11                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   19 13
  6P GAIN WILD-TYPE 69 41
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               32               110 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               13                41 
$`6P GAIN MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GO 
       25.78        31.27        14.30         7.63        13.94        16.24 
TCGA-IG-A4QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-L5-A43E 
        0.26         0.46         0.43       122.10        68.02         3.45 
TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 
        4.08        30.74         6.94         2.60         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT 
       55.50         2.66        12.92         5.42        21.37        27.12 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A4MQ TCGA-R6-A6L4 
       10.36        10.45         0.13         0.10         0.10        14.70 
TCGA-R6-A6L6 TCGA-VR-AA7I 
        7.04        15.91 

$`6P GAIN WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       58.55         5.92         8.94         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12         0.03 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        0.99         0.53        17.03         0.79        23.41         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG 
        0.13        14.86        44.75        60.39         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        15.48        23.18        25.28        18.08 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       17.59         6.21         3.16         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.52         3.68         3.35        19.50         8.78         6.41 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y 
       29.00         7.13         7.43         8.71        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        7.40        35.97        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        7.76         8.71        13.41        83.24        52.57        46.09 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
        0.07         0.16         0.07         0.33         0.10         0.07 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10         0.07         0.07         0.13         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10         0.10         0.07         0.07         0.07         0.20 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        1.18        17.62         5.16         3.78         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO 
        5.06        29.59         6.35        53.95         9.30         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        8.78        14.01         5.29         3.42         4.80         8.48 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.15         4.44        18.31         8.12        36.72        12.03 
TCGA-VR-AA7D TCGA-ZR-A9CJ 
        9.17        18.12 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.10              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           122.10             83.24 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            8.995             7.415 
[1] "0.1 - 122.1 (9.0)" "0.0 - 83.2 (7.4)" 
[1] "hr=" "1.1"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED         3        1        1        0         8         5
  6P GAIN WILD-TYPE       5        3        5        1        27        21
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           7          0          2          1        1
  6P GAIN WILD-TYPE        16         11          6          5        2
                   vv
clus                STAGE IVA
  6P GAIN MUTATED           2
  6P GAIN WILD-TYPE         0
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  3                 5
  STAGE IA                 1                 3
  STAGE IB                 1                 5
  STAGE II                 0                 1
  STAGE IIA                8                27
  STAGE IIB                5                21
  STAGE III                7                16
  STAGE IIIA               0                11
  STAGE IIIB               2                 6
  STAGE IIIC               1                 5
  STAGE IV                 1                 2
  STAGE IVA                2                 0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  6P GAIN MUTATED       8  6 17  1
  6P GAIN WILD-TYPE    18 27 57  3
D11V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1               8                18
  T2                  6                27
  T3                 17                57
  T4                  1                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  6P GAIN MUTATED   16 12  2  1
  6P GAIN WILD-TYPE 48 42  9  5
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              16                48
  N1              12                42
  N2               2                 9
  N3               1                 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                M0 M1 M1A MX
  6P GAIN MUTATED   25  1   2  3
  6P GAIN WILD-TYPE 86  1   1 14
D11V6, multiclass
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0               25                86
  M1                1                 1
  M1A               2                 1
  MX                3                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    4 30
  6P GAIN WILD-TYPE 17 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4   30
  6P GAIN WILD-TYPE   17   99
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               4                17
  MALE                30                99
[1] 2 2
[1] FALSE
D11V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       9                         0    19
  6P GAIN WILD-TYPE    29                         2    74
D11V9, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   9                29
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  19                74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED   15 12
  6Q GAIN WILD-TYPE 73 42
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               27               115 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               12                42 
$`6Q GAIN MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IG-A4QS 
       31.27        14.30         7.63        13.94        16.24         0.26 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A88S 
        0.43       122.10        60.39        68.02         3.45         6.94 
TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NQ 
        2.60         3.02        55.50         2.66        12.92        21.37 
TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A4MQ 
       27.12        10.36        10.45         0.13         0.10         0.10 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-VR-AA7I 
       14.70         7.04        15.91 

$`6Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR 
       25.78        58.55         5.92         8.94         4.21        32.45 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        0.03         0.99         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FE 
        0.36         0.13        14.86         0.46        44.75         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        15.48        23.18        25.28 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J 
       18.08        17.59         6.21         3.16         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        8.94         3.52         3.68         3.35        19.50         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
        6.41         4.08        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        30.74         4.90        29.00         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG 
        8.71        25.12         0.36         7.40         3.95        35.97 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.42 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K 
        8.71        13.41        83.24        52.57        46.09         0.07 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V 
        0.16         0.07         0.33         0.10         0.07         0.10 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.07         0.07         0.13         0.07         0.10         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.07         0.07         0.07         0.20         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       17.62         5.16         3.78         8.02         7.59         5.06 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
       29.59         6.35        53.95         9.30         7.00         8.78 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       14.01         5.29         3.42         4.80         8.48         8.15 
TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
        4.44        18.31         8.12        36.72        12.03         9.17 
TCGA-ZR-A9CJ 
       18.12 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.10              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           122.10             83.24 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            10.45              7.17 
[1] "0.1 - 122.1 (10.4)" "0.0 - 83.2 (7.2)"  
[1] "hr=" "1.2"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED         4        0        1        0         7         4
  6Q GAIN WILD-TYPE       4        4        5        1        28        22
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED           5          0          1          1        1
  6Q GAIN WILD-TYPE        18         11          7          5        2
                   vv
clus                STAGE IVA
  6Q GAIN MUTATED           2
  6Q GAIN WILD-TYPE         0
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  4                 4
  STAGE IA                 0                 4
  STAGE IB                 1                 5
  STAGE II                 0                 1
  STAGE IIA                7                28
  STAGE IIB                4                22
  STAGE III                5                18
  STAGE IIIA               0                11
  STAGE IIIB               1                 7
  STAGE IIIC               1                 5
  STAGE IV                 1                 2
  STAGE IVA                2                 0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  6Q GAIN MUTATED       8  4 13  1
  6Q GAIN WILD-TYPE    18 29 61  3
D12V4, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1               8                18
  T2                  4                29
  T3                 13                61
  T4                  1                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  6Q GAIN MUTATED   15  8  1  1
  6Q GAIN WILD-TYPE 49 46 10  5
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              15                49
  N1               8                46
  N2               1                10
  N3               1                 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                M0 M1 M1A MX
  6Q GAIN MUTATED   20  1   2  3
  6Q GAIN WILD-TYPE 91  1   1 14
D12V6, multiclass
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0               20                91
  M1                1                 1
  M1A               2                 1
  MX                3                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     2  26
  6Q GAIN WILD-TYPE  19 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2   26
  6Q GAIN WILD-TYPE   19  103
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               2                19
  MALE                26               103
[1] 2 2
[1] FALSE
D12V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       7                         0    16
  6Q GAIN WILD-TYPE    31                         2    77
D12V9, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   7                31
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  16                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   56 32
  7P GAIN WILD-TYPE 32 22
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               88                54 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               32                22 
$`7P GAIN MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78         5.92        13.94         8.94        16.24        32.45 
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D 
       20.09         2.63        20.12         0.03         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FB TCGA-JY-A939 TCGA-JY-A93C 
        0.79        23.41         0.43        60.39        15.48        23.18 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE 
       18.08         3.16         3.45         0.30         4.31         3.52 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        3.68         3.35        19.50        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
        3.16        30.74         4.90         7.13         6.94         2.60 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        0.36         3.95         3.02         2.66        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NT 
       16.47        13.55        13.22         5.42         8.71        27.12 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O 
       52.57        46.09        10.36         0.07         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 
        0.10         0.07         0.10         0.07         0.10         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.07         0.10         0.10         0.10         0.07         0.20 
TCGA-LN-A5U7 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        1.18         3.78         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO 
        7.04        29.59         6.35        53.95         9.30         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       14.01         5.29         3.42         8.48         8.15         4.44 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA7I TCGA-ZR-A9CJ 
       18.31         8.12        15.91        18.12 

$`7P GAIN WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GQ TCGA-IG-A3I8 
       31.27        14.30        58.55         7.63         4.21        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A6QS 
        0.85        20.78         0.26         0.99         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.86         0.46       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        42.77        25.41        25.28        17.59         6.21 
TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OU 
        8.94         8.78         6.41         4.08         7.17        29.00 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NI 
        7.43         8.71        25.12         7.40        55.50        13.48 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M 
        7.76        21.37        13.41        83.24        10.45         0.16 
TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-M9-A5M8 
        0.13         0.07         0.10         0.07         0.07        17.62 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-V5-A7RE TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
        5.16         8.78         4.80        36.72        12.03         9.17 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.03              0.07 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            60.39            122.10 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            6.135             8.860 
[1] "0.0 - 60.4 (6.1)"  "0.1 - 122.1 (8.9)"
[1] "hr=" "1.4"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED         5        1        4        1        14        16
  7P GAIN WILD-TYPE       3        3        2        0        21        10
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED          16          5          4          3        3
  7P GAIN WILD-TYPE         7          6          4          3        0
                   vv
clus                STAGE IVA
  7P GAIN MUTATED           2
  7P GAIN WILD-TYPE         0
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  5                 3
  STAGE IA                 1                 3
  STAGE IB                 4                 2
  STAGE II                 1                 0
  STAGE IIA               14                21
  STAGE IIB               16                10
  STAGE III               16                 7
  STAGE IIIA               5                 6
  STAGE IIIB               4                 4
  STAGE IIIC               3                 3
  STAGE IV                 3                 0
  STAGE IVA                2                 0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  7P GAIN MUTATED      17 12 47  1
  7P GAIN WILD-TYPE     9 21 27  3
D13V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1              17                 9
  T2                 12                21
  T3                 47                27
  T4                  1                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  7P GAIN MUTATED   32 36  5  3
  7P GAIN WILD-TYPE 32 18  6  3
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              32                32
  N1              36                18
  N2               5                 6
  N3               3                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  7P GAIN MUTATED   58  2   3 11
  7P GAIN WILD-TYPE 53  0   0  6
D13V6, multiclass
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0               58                53
  M1                2                 0
  M1A               3                 0
  MX               11                 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"
D13V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    9 81
  7P GAIN WILD-TYPE 12 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      9   81
  7P GAIN WILD-TYPE   12   48
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               9                12
  MALE                81                48
[1] 2 2
[1] FALSE
D13V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED      22                         2    57
  7P GAIN WILD-TYPE    16                         0    36
D13V9, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                  22                16
  BLACK OR AFRICAN AMERICAN               2                 0
  WHITE                                  57                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"

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   49 21
  7Q GAIN WILD-TYPE 39 33
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               70                72 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               21                33 
$`7Q GAIN MUTATED`
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A4P3 
        8.94        16.24        32.45        20.09        20.12         0.03 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FB TCGA-JY-A939 TCGA-JY-A93C 
       17.03        23.41         0.43        60.39        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       25.28        18.08         3.16         3.45         0.30         4.31 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO 
        3.52         3.68         3.35        19.50         4.08         3.32 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 
        3.16         4.90         6.94         2.60         0.36         3.95 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NT 
        3.02         2.66        35.97        13.22         5.42        27.12 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49R 
       52.57        46.09        10.36         0.07         0.33         0.10 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
        0.07         0.10         0.07         0.13         0.07         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.07         0.07         0.10         0.07         0.20         1.18 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        3.78         8.02        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
        9.30         7.00        14.01         5.29         3.42         8.48 
TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8EW TCGA-ZR-A9CJ 
        8.15        18.31         8.12        18.12 

$`7Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       13.94         4.21        33.27         0.85        20.78         2.63 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        0.26         0.99         0.53         0.79         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.86         0.46       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43M 
       41.52        42.77        25.41        17.59         6.21         8.94 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
        8.78         6.41        18.35         7.17         1.38        30.74 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.13         7.43         8.71        25.12         7.40 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
       55.50        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M 
       21.37         8.71        13.41        83.24        10.45         0.16 
TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.07         0.13         0.10         0.07         0.10         0.10 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-S8-A6BV 
       17.62         5.16         7.59         5.06        53.95         8.78 
TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        4.80         4.44        36.72        12.03         9.17        15.91 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.03              0.07 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            60.39            122.10 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            5.095             8.780 
[1] "0.0 - 60.4 (5.1)"  "0.1 - 122.1 (8.8)"
[1] "hr=" "1"  
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED         5        2        3        1        14        11
  7Q GAIN WILD-TYPE       3        2        3        0        21        15
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED          10          2          4          4        2
  7Q GAIN WILD-TYPE        13          9          4          2        1
                   vv
clus                STAGE IVA
  7Q GAIN MUTATED           2
  7Q GAIN WILD-TYPE         0
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  5                 3
  STAGE IA                 2                 2
  STAGE IB                 3                 3
  STAGE II                 1                 0
  STAGE IIA               14                21
  STAGE IIB               11                15
  STAGE III               10                13
  STAGE IIIA               2                 9
  STAGE IIIB               4                 4
  STAGE IIIC               4                 2
  STAGE IV                 2                 1
  STAGE IVA                2                 0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  7Q GAIN MUTATED      15 11 37  0
  7Q GAIN WILD-TYPE    11 22 37  4
D14V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1              15                11
  T2                 11                22
  T3                 37                37
  T4                  0                 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                N0 N1 N2 N3
  7Q GAIN MUTATED   30 24  4  4
  7Q GAIN WILD-TYPE 34 30  7  2
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              30                34
  N1              24                30
  N2               4                 7
  N3               4                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  7Q GAIN MUTATED   46  1   3 10
  7Q GAIN WILD-TYPE 65  1   0  7
D14V6, multiclass
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0               46                65
  M1                1                 1
  M1A               3                 0
  MX               10                 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"
D14V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    5 67
  7Q GAIN WILD-TYPE 16 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5   67
  7Q GAIN WILD-TYPE   16   62
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               5                16
  MALE                67                62
[1] 2 2
[1] FALSE
D14V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED      20                         2    46
  7Q GAIN WILD-TYPE    18                         0    47
D14V9, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                  20                18
  BLACK OR AFRICAN AMERICAN               2                 0
  WHITE                                  46                47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   31 23
  8P GAIN WILD-TYPE 57 31
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               54                88 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               23                31 
$`8P GAIN MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       14.30         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6F8 
       20.09        20.78        17.03         0.36         0.46       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E 
       68.02         3.68        25.28        17.59         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
        0.30         4.31         8.78         4.08        18.35         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NG 
        3.16         4.90         7.13         2.60         0.36        35.97 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L7-A6VZ 
       13.55        13.22         7.76        21.37        13.41        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
        0.07        10.45         0.33         0.13         0.07         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.07         0.10         0.10         0.10         7.59         5.06 
TCGA-R6-A6L6 TCGA-RE-A7BO TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EW TCGA-ZR-A9CJ 
        7.04         7.00         4.80         8.48         8.12        18.12 

$`8P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85         2.63        20.12         0.03         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
        0.53         0.79        23.41         0.13        14.86         0.43 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       44.75        60.39        41.52        42.77        25.41        15.48 
TCGA-JY-A93C TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       23.18        18.08         6.21         8.94         3.52         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS 
        3.35        19.50         6.41         3.32         7.17        30.74 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.43         6.94         8.71        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.95         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       16.47         5.42         8.71        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A2 
       46.09         0.16         0.07         0.10         0.07         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.07         0.10         0.07         0.07         0.10         0.07 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.20         1.18        17.62         5.16         3.78         8.02 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BV 
       14.70        29.59         6.35        53.95         9.30         8.78 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU 
       14.01         5.29         3.42         8.15         4.44        18.31 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       36.72        12.03         9.17        15.91 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.07              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           122.10             83.24 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            7.085             7.825 
[1] "0.1 - 122.1 (7.1)" "0.0 - 83.2 (7.8)" 
[1] "hr=" "1.4"
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED         2        2        2        1        13         9
  8P GAIN WILD-TYPE       6        2        4        0        22        17
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED          11          2          3          4        1
  8P GAIN WILD-TYPE        12          9          5          2        2
                   vv
clus                STAGE IVA
  8P GAIN MUTATED           1
  8P GAIN WILD-TYPE         1
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 2                 2
  STAGE IB                 2                 4
  STAGE II                 1                 0
  STAGE IIA               13                22
  STAGE IIB                9                17
  STAGE III               11                12
  STAGE IIIA               2                 9
  STAGE IIIB               3                 5
  STAGE IIIC               4                 2
  STAGE IV                 1                 2
  STAGE IVA                1                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  8P GAIN MUTATED       9  9 33  1
  8P GAIN WILD-TYPE    17 24 41  3
D15V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1               9                17
  T2                  9                24
  T3                 33                41
  T4                  1                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  8P GAIN MUTATED   26 18  4  4
  8P GAIN WILD-TYPE 38 36  7  2
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              26                38
  N1              18                36
  N2               4                 7
  N3               4                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  8P GAIN MUTATED   39  0   2  9
  8P GAIN WILD-TYPE 72  2   1  8
D15V6, multiclass
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               39                72
  M1                0                 2
  M1A               2                 1
  MX                9                 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"
D15V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    9 47
  8P GAIN WILD-TYPE 12 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9   47
  8P GAIN WILD-TYPE   12   82
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               9                12
  MALE                47                82
[1] 2 2
[1] FALSE
D15V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED      16                         1    33
  8P GAIN WILD-TYPE    22                         1    60
D15V9, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                  16                22
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  33                60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   47 29
  8Q GAIN WILD-TYPE 41 25
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               76                66 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               29                25 
$`8Q GAIN MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
       14.30        13.94         8.94        16.24         4.21        32.45 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
       33.27        20.09        20.78         2.63        20.12         0.26 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD 
       17.03         0.36         0.46         0.43       122.10        68.02 
TCGA-JY-A6FE TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E 
        3.68        23.18        25.28        17.59         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30         4.31         8.78         4.08        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
        1.38         3.16         4.90         7.13         7.43         2.60 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        0.36        35.97        13.55        13.22         7.76         5.42 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ 
       21.37         8.71        13.41        27.12        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        0.07        10.45         0.33         0.10         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 
        0.10         0.07         0.10         0.10         0.10         0.07 
TCGA-LN-A4MQ TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-RE-A7BO 
        0.10         7.59         5.06         7.04        53.95         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        8.78        14.01         4.80         8.48         8.15         4.44 
TCGA-VR-A8EW TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        8.12         9.17        15.91        18.12 

$`8Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-IG-A3Y9 
       25.78        31.27        58.55         7.63         5.92         0.85 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
        0.03         0.99         0.53         0.79        23.41         0.13 
TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       14.86        44.75        60.39        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       15.48        18.08         6.21         8.94         3.52         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OU 
        3.35        19.50         6.41         7.17        30.74        29.00 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        6.94         8.71        25.12         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NU 
       55.50         2.66        12.92        13.48        16.47        83.24 
TCGA-L5-A8NV TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       52.57         0.16         0.07         0.07         0.13         0.07 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 
        0.10         0.07         0.07         0.20         1.18        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ 
        5.16         3.78         8.02        14.70        29.59         6.35 
TCGA-R6-A6Y2 TCGA-V5-A7RB TCGA-V5-A7RC TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G 
        9.30         5.29         3.42        18.31        36.72        12.03 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.07              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           122.10             83.24 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            7.510             7.515 
[1] "0.1 - 122.1 (7.5)" "0.0 - 83.2 (7.5)" 
[1] "hr=" "1.2"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED         2        2        4        1        18        12
  8Q GAIN WILD-TYPE       6        2        2        0        17        14
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED          16          5          5          6        1
  8Q GAIN WILD-TYPE         7          6          3          0        2
                   vv
clus                STAGE IVA
  8Q GAIN MUTATED           1
  8Q GAIN WILD-TYPE         1
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 2                 2
  STAGE IB                 4                 2
  STAGE II                 1                 0
  STAGE IIA               18                17
  STAGE IIB               12                14
  STAGE III               16                 7
  STAGE IIIA               5                 6
  STAGE IIIB               5                 3
  STAGE IIIC               6                 0
  STAGE IV                 1                 2
  STAGE IVA                1                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  8Q GAIN MUTATED      10 14 48  2
  8Q GAIN WILD-TYPE    16 19 26  2
D16V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1              10                16
  T2                 14                19
  T3                 48                26
  T4                  2                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  8Q GAIN MUTATED   33 28  6  6
  8Q GAIN WILD-TYPE 31 26  5  0
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              33                31
  N1              28                26
  N2               6                 5
  N3               6                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  8Q GAIN MUTATED   59  0   2 11
  8Q GAIN WILD-TYPE 52  2   1  6
D16V6, multiclass
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0               59                52
  M1                0                 2
  M1A               2                 1
  MX               11                 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"
D16V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   10 71
  8Q GAIN WILD-TYPE 11 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     10   71
  8Q GAIN WILD-TYPE   11   58
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              10                11
  MALE                71                58
[1] 2 2
[1] FALSE
D16V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED      24                         1    47
  8Q GAIN WILD-TYPE    14                         1    46
D16V9, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                  24                14
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  47                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    8  3
  9P GAIN WILD-TYPE 80 51
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               11               131 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                51 
$`9P GAIN MUTATED`
TCGA-2H-A9GL TCGA-IG-A625 TCGA-JY-A6F8 TCGA-L5-A4OU TCGA-L5-A88Y TCGA-L5-A8NT 
        5.92         0.36       122.10        29.00         0.36        27.12 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49V TCGA-VR-AA4G TCGA-VR-AA7D 
        0.33         0.10         0.10        12.03         9.17 

$`9P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12         0.03         0.26 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
        0.99         0.53        17.03         0.79        23.41         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86         0.46         0.43        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.68        41.52        42.77        25.41        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       25.28        18.08        17.59         6.21         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        0.30         4.31         8.94         3.52         3.68         3.35 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       19.50         8.78         6.41         4.08        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW 
        7.17         1.38         3.16        30.74         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.43         6.94         8.71         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.42 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S 
       10.36         0.07        10.45         0.16         0.07         0.13 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.07         0.07         0.10         0.07         0.13         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10         0.10         0.10         0.07         0.07         0.10 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.07         0.20         1.18        17.62         5.16         3.78 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        6.35        53.95         9.30         7.00         8.78        14.01 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42         4.80         8.48         8.15         4.44 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-ZR-A9CJ 
       18.31         8.12        36.72        15.91        18.12 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.10              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           122.10             83.24 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             5.92              7.59 
[1] "0.1 - 122.1 (5.9)" "0.0 - 83.2 (7.6)" 
[1] "hr=" "1.6"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P GAIN MUTATED         1        0        0        0         4         1
  9P GAIN WILD-TYPE       7        4        6        1        31        25
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED           2          1          1          1        0
  9P GAIN WILD-TYPE        21         10          7          5        3
                   vv
clus                STAGE IVA
  9P GAIN MUTATED           0
  9P GAIN WILD-TYPE         2
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 4
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                4                31
  STAGE IIB                1                25
  STAGE III                2                21
  STAGE IIIA               1                10
  STAGE IIIB               1                 7
  STAGE IIIC               1                 5
  STAGE IV                 0                 3
  STAGE IVA                0                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  9P GAIN MUTATED       2  1  9  0
  9P GAIN WILD-TYPE    24 32 65  4
D17V4, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1               2                24
  T2                  1                32
  T3                  9                65
  T4                  0                 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                N0 N1 N2 N3
  9P GAIN MUTATED    7  2  2  1
  9P GAIN WILD-TYPE 57 52  9  5
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0               7                57
  N1               2                52
  N2               2                 9
  N3               1                 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                 M0  M1 M1A  MX
  9P GAIN MUTATED    11   0   0   1
  9P GAIN WILD-TYPE 100   2   3  16
D17V6, multiclass
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0               11               100
  M1                0                 2
  M1A               0                 3
  MX                1                16
[1] 4 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  11
  9P GAIN WILD-TYPE  20 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   11
  9P GAIN WILD-TYPE   20  118
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               1                20
  MALE                11               118
[1] 2 2
[1] FALSE
D17V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       5                         0     5
  9P GAIN WILD-TYPE    33                         2    88
D17V9, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   5                33
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                   5                88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED   18  4
  9Q GAIN WILD-TYPE 70 50
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               22               120 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4                50 
$`9Q GAIN MUTATED`
TCGA-2H-A9GL TCGA-IG-A50L TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-L5-A43C 
        5.92         0.53         0.36       122.10        60.39         3.16 
TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L5-A88Y TCGA-L5-A8NT TCGA-LN-A49K TCGA-LN-A49O 
        3.32        29.00         0.36        27.12         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10         0.10         0.10         0.13         0.07         0.10 
TCGA-R6-A6L4 TCGA-S8-A6BV TCGA-VR-AA4G TCGA-VR-AA7D 
       14.70         8.78        12.03         9.17 

$`9Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12         0.03         0.26 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.99        17.03         0.79        23.41         0.13        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        0.46         0.43        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        15.48        23.18        25.28        18.08 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       17.59         6.21         3.45         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.52         3.68         3.35        19.50         8.78         6.41 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        4.08        18.35         7.17         1.38         3.16        30.74 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        4.90         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.42        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       52.57        46.09        10.36        10.45         0.16         0.07 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.13         0.07         0.07         0.07         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.10         0.07         0.07         0.20         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       17.62         5.16         3.78         8.02         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO 
        7.04        29.59         6.35        53.95         9.30         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       14.01         5.29         3.42         4.80         8.48         8.15 
TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-ZR-A9CJ 
        4.44        18.31         8.12        36.72        15.91        18.12 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.07              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           122.10             83.24 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            1.845             7.890 
[1] "0.1 - 122.1 (1.8)" "0.0 - 83.2 (7.9)" 
[1] "hr=" "2"  
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         2        0        0        0         8         1
  9Q GAIN WILD-TYPE       6        4        6        1        27        25
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED           3          3          1          2        0
  9Q GAIN WILD-TYPE        20          8          7          4        3
                   vv
clus                STAGE IVA
  9Q GAIN MUTATED           0
  9Q GAIN WILD-TYPE         2
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 0                 4
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                8                27
  STAGE IIB                1                25
  STAGE III                3                20
  STAGE IIIA               3                 8
  STAGE IIIB               1                 7
  STAGE IIIC               2                 4
  STAGE IV                 0                 3
  STAGE IVA                0                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  9Q GAIN MUTATED       3  2 16  0
  9Q GAIN WILD-TYPE    23 31 58  4
D18V4, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1               3                23
  T2                  2                31
  T3                 16                58
  T4                  0                 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                N0 N1 N2 N3
  9Q GAIN MUTATED   12  5  2  2
  9Q GAIN WILD-TYPE 52 49  9  4
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              12                52
  N1               5                49
  N2               2                 9
  N3               2                 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                M0 M1 M1A MX
  9Q GAIN MUTATED   19  0   0  2
  9Q GAIN WILD-TYPE 92  2   3 15
D18V6, multiclass
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0               19                92
  M1                0                 2
  M1A               0                 3
  MX                2                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1  22
  9Q GAIN WILD-TYPE  20 107
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   22
  9Q GAIN WILD-TYPE   20  107
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               1                20
  MALE                22               107
[1] 2 2
[1] FALSE
D18V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED      11                         0    10
  9Q GAIN WILD-TYPE    27                         2    83
D18V9, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                  11                27
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  10                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED   18 11
  10P GAIN WILD-TYPE 70 43
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                29                113 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                11                 43 
$`10P GAIN MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3YC TCGA-JY-A6F8 
       58.55        13.94        16.24        32.45        20.12       122.10 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OH TCGA-L5-A4OR TCGA-L5-A88V TCGA-L5-A893 
       18.08         3.16        19.50         3.16         2.60         3.02 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NR TCGA-L7-A6VZ TCGA-LN-A49L 
       55.50        12.92        16.47         8.71        10.36        10.45 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-R6-A6DN TCGA-R6-A6KZ 
        0.10         0.13         0.10         0.20         8.02         5.06 
TCGA-R6-A6XQ TCGA-S8-A6BW TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8Q7 
        6.35        14.01         8.15        18.31        36.72 

$`10P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        14.30         7.63         5.92         8.94 
TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        4.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
        0.03         0.26         0.99         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41         0.36         0.13        14.86         0.46         0.43 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       25.41        15.48        23.18        25.28        17.59         6.21 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.45         0.30         4.31         8.94         3.52         3.68 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        3.35         8.78         6.41         4.08        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38        30.74         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        7.43         6.94         8.71        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
        3.95         2.66        35.97        13.48        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        7.76         5.42        21.37        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       52.57        46.09         0.07         0.16         0.07         0.33 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        0.07         0.10         0.07         0.10         0.07         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.07         0.10         0.10         0.07         0.07         0.10 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ 
        0.07         1.18        17.62         5.16         3.78         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO 
       14.70         7.04        29.59        53.95         9.30         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        8.78         5.29         3.42         4.80         8.48         4.44 
TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        8.12        12.03         9.17        15.91        18.12 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.10               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            122.10              83.24 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             10.45               7.04 
[1] "0.1 - 122.1 (10.4)" "0.0 - 83.2 (7.0)"  
[1] "hr=" "1.4"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P GAIN MUTATED         4        1        1        1         5         3
  10P GAIN WILD-TYPE       4        3        5        0        30        23
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED           4          3          0          1        2
  10P GAIN WILD-TYPE        19          8          8          5        1
                    vv
clus                 STAGE IVA
  10P GAIN MUTATED           1
  10P GAIN WILD-TYPE         1
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  1                  3
  STAGE IB                  1                  5
  STAGE II                  1                  0
  STAGE IIA                 5                 30
  STAGE IIB                 3                 23
  STAGE III                 4                 19
  STAGE IIIA                3                  8
  STAGE IIIB                0                  8
  STAGE IIIC                1                  5
  STAGE IV                  2                  1
  STAGE IVA                 1                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  10P GAIN MUTATED       8  6 12  0
  10P GAIN WILD-TYPE    18 27 62  4
D19V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1                8                 18
  T2                   6                 27
  T3                  12                 62
  T4                   0                  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                 N0 N1 N2 N3
  10P GAIN MUTATED   13 12  0  1
  10P GAIN WILD-TYPE 51 42 11  5
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               13                 51
  N1               12                 42
  N2                0                 11
  N3                1                  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                 M0 M1 M1A MX
  10P GAIN MUTATED   19  2   1  4
  10P GAIN WILD-TYPE 92  0   2 13
D19V6, multiclass
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                19                 92
  M1                 2                  0
  M1A                1                  2
  MX                 4                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     2  29
  10P GAIN WILD-TYPE  19 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2   29
  10P GAIN WILD-TYPE   19  100
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                2                 19
  MALE                 29                100
[1] 2 2
[1] FALSE
D19V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       7                         0    19
  10P GAIN WILD-TYPE    31                         2    74
D19V9, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    7                 31
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   19                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED   12 11
  10Q GAIN WILD-TYPE 76 43
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                23                119 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                11                 43 
$`10Q GAIN MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IG-A5B8 TCGA-JY-A6F8 TCGA-JY-A93E 
       58.55        13.94        16.24         0.79       122.10        18.08 
TCGA-L5-A43J TCGA-L5-A4OH TCGA-L5-A4OR TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH 
        4.31        19.50         3.16         3.02        55.50        12.92 
TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49V TCGA-R6-A6DN 
       16.47        10.36        10.45         0.13         0.10         8.02 
TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-S8-A6BW TCGA-VR-A8Q7 TCGA-ZR-A9CJ 
        5.06         6.35        14.01        36.72        18.12 

$`10Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        14.30         7.63         5.92         8.94 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12         0.03         0.26         0.99         0.53 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03        23.41         0.36         0.13        14.86         0.46 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        0.43        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       42.77        25.41        15.48        23.18        25.28        17.59 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE 
        6.21         3.16         3.45         0.30         8.94         3.52 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.68         3.35         8.78         6.41         4.08        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI 
        0.36         7.40         3.95         2.66        35.97        13.48 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.42        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K 
       13.41        27.12        83.24        52.57        46.09         0.07 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W 
        0.16         0.07         0.33         0.10         0.07         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10         0.07         0.13         0.07         0.10         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10         0.07         0.07         0.10         0.07         0.20 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 
        1.18        17.62         5.16         3.78         7.59        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
        7.04        29.59        53.95         9.30         7.00         8.78 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42         4.80         8.48         8.15         4.44 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       18.31         8.12        12.03         9.17        15.91 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.10               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            122.10              83.24 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             12.92               7.13 
[1] "0.1 - 122.1 (12.9)" "0.0 - 83.2 (7.1)"  
[1] "hr=" "1.1"
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q GAIN MUTATED         4        1        2        0         4         3
  10Q GAIN WILD-TYPE       4        3        4        1        31        23
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED           1          2          0          2        1
  10Q GAIN WILD-TYPE        22          9          8          4        2
                    vv
clus                 STAGE IVA
  10Q GAIN MUTATED           1
  10Q GAIN WILD-TYPE         1
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  1                  3
  STAGE IB                  2                  4
  STAGE II                  0                  1
  STAGE IIA                 4                 31
  STAGE IIB                 3                 23
  STAGE III                 1                 22
  STAGE IIIA                2                  9
  STAGE IIIB                0                  8
  STAGE IIIC                2                  4
  STAGE IV                  1                  2
  STAGE IVA                 1                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  10Q GAIN MUTATED       7  3 11  0
  10Q GAIN WILD-TYPE    19 30 63  4
D20V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T0+T1                7                 19
  T2                   3                 30
  T3                  11                 63
  T4                   0                  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                 N0 N1 N2 N3
  10Q GAIN MUTATED   13  6  0  2
  10Q GAIN WILD-TYPE 51 48 11  4
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               13                 51
  N1                6                 48
  N2                0                 11
  N3                2                  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                 M0 M1 M1A MX
  10Q GAIN MUTATED   14  1   1  5
  10Q GAIN WILD-TYPE 97  1   2 12
D20V6, multiclass
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                14                 97
  M1                 1                  1
  M1A                1                  2
  MX                 5                 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"
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1  23
  10Q GAIN WILD-TYPE  20 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1   23
  10Q GAIN WILD-TYPE   20  106
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                1                 20
  MALE                 23                106
[1] 2 2
[1] FALSE
D20V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       4                         0    17
  10Q GAIN WILD-TYPE    34                         2    76
D20V9, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    4                 34
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   17                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED   17 15
  11P GAIN WILD-TYPE 71 39
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                32                110 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                15                 39 
$`11P GAIN MUTATED`
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB 
        8.94        16.24        23.41         0.43       122.10        60.39 
TCGA-JY-A6FE TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON 
        3.68         8.94         3.52         3.68         4.08        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A8NF TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV 
        1.38        29.00         2.66         5.42        27.12        52.57 
TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4MQ TCGA-LN-A4MR 
       46.09         0.07         0.10         0.07         0.10         0.07 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-RE-A7BO TCGA-V5-A7RC TCGA-VR-A8EW 
        3.78         7.59         7.04         7.00         3.42         8.12 
TCGA-VR-AA7I TCGA-ZR-A9CJ 
       15.91        18.12 

$`11P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       13.94         4.21        32.45        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12         0.03         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03         0.79         0.36         0.13        14.86 
TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
        0.46        44.75        68.02        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       15.48        23.18        25.28        18.08        17.59         6.21 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OH 
        3.16         3.45         0.30         4.31         3.35        19.50 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
        8.78         6.41         3.32         7.17         3.16        30.74 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        4.90         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ 
        7.76        21.37         8.71        13.41        83.24        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45         0.16         0.07         0.33         0.10         0.13 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.07         0.07         0.10         0.13         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.10         0.07         0.07         0.20         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
       17.62         5.16         8.02         5.06        14.70        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        6.35        53.95         9.30         8.78        14.01         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8Q7 
        4.80         8.48         8.15         4.44        18.31        36.72 
TCGA-VR-AA4G TCGA-VR-AA7D 
       12.03         9.17 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.07               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            122.10              83.24 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             7.020              7.695 
[1] "0.1 - 122.1 (7.0)" "0.0 - 83.2 (7.7)" 
[1] "hr=" "1.2"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED         2        1        1        0         8         5
  11P GAIN WILD-TYPE       6        3        5        1        27        21
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           5          1          3          1        0
  11P GAIN WILD-TYPE        18         10          5          5        3
                    vv
clus                 STAGE IVA
  11P GAIN MUTATED           2
  11P GAIN WILD-TYPE         0
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  1                  3
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 8                 27
  STAGE IIB                 5                 21
  STAGE III                 5                 18
  STAGE IIIA                1                 10
  STAGE IIIB                3                  5
  STAGE IIIC                1                  5
  STAGE IV                  0                  3
  STAGE IVA                 2                  0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  11P GAIN MUTATED       7  3 19  1
  11P GAIN WILD-TYPE    19 30 55  3
D21V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1                7                 19
  T2                   3                 30
  T3                  19                 55
  T4                   1                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  11P GAIN MUTATED   14  9  5  1
  11P GAIN WILD-TYPE 50 45  6  5
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               14                 50
  N1                9                 45
  N2                5                  6
  N3                1                  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                 M0 M1 M1A MX
  11P GAIN MUTATED   21  0   2  3
  11P GAIN WILD-TYPE 90  2   1 14
D21V6, multiclass
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                21                 90
  M1                 0                  2
  M1A                2                  1
  MX                 3                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     5  28
  11P GAIN WILD-TYPE  16 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5   28
  11P GAIN WILD-TYPE   16  101
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                5                 16
  MALE                 28                101
[1] 2 2
[1] FALSE
D21V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       8                         1    21
  11P GAIN WILD-TYPE    30                         1    72
D21V9, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    8                 30
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   21                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED   17  8
  11Q GAIN WILD-TYPE 71 46
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                25                117 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                 46 
$`11Q GAIN MUTATED`
TCGA-IG-A51D TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-L5-A43M 
       17.03         0.43       122.10        60.39         3.68         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OU 
        3.52         3.68        19.50        18.35         1.38        29.00 
TCGA-L5-A88Y TCGA-L5-A8NN TCGA-LN-A49K TCGA-LN-A49Y TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.36         5.42         0.07         0.07         0.10         0.07 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-RE-A7BO TCGA-V5-AASW TCGA-VR-A8EW 
        3.78         7.59         7.04         7.00         8.15         8.12 
TCGA-ZR-A9CJ 
       18.12 

$`11Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12         0.03 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        0.26         0.99         0.53         0.79        23.41         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
        0.13        14.86         0.46        44.75        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        15.48        23.18        25.28        18.08 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       17.59         6.21         3.16         3.45         0.30         4.31 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
        3.35         8.78         6.41         4.08         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        30.74         4.90         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
       55.50         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         7.76        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L 
       27.12        83.24        52.57        46.09        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        0.16         0.07         0.33         0.10         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10         0.07         0.10         0.13         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.10         0.07         0.07         0.20         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
       17.62         5.16         8.02         5.06        14.70        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        6.35        53.95         9.30         8.78        14.01         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8Q7 
        3.42         4.80         8.48         4.44        18.31        36.72 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       12.03         9.17        15.91 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.07               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            122.10              83.24 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              7.00               7.76 
[1] "0.1 - 122.1 (7.0)" "0.0 - 83.2 (7.8)" 
[1] "hr=" "1.2"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         3        0        0        0         5         4
  11Q GAIN WILD-TYPE       5        4        6        1        30        22
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           3          1          3          1        0
  11Q GAIN WILD-TYPE        20         10          5          5        3
                    vv
clus                 STAGE IVA
  11Q GAIN MUTATED           0
  11Q GAIN WILD-TYPE         2
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  0                  4
  STAGE IB                  0                  6
  STAGE II                  0                  1
  STAGE IIA                 5                 30
  STAGE IIB                 4                 22
  STAGE III                 3                 20
  STAGE IIIA                1                 10
  STAGE IIIB                3                  5
  STAGE IIIC                1                  5
  STAGE IV                  0                  3
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  11Q GAIN MUTATED       8  2 12  0
  11Q GAIN WILD-TYPE    18 31 62  4
D22V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1                8                 18
  T2                   2                 31
  T3                  12                 62
  T4                   0                  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                 N0 N1 N2 N3
  11Q GAIN MUTATED    8  7  5  1
  11Q GAIN WILD-TYPE 56 47  6  5
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                8                 56
  N1                7                 47
  N2                5                  6
  N3                1                  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                 M0 M1 M1A MX
  11Q GAIN MUTATED   15  0   0  4
  11Q GAIN WILD-TYPE 96  2   3 13
D22V6, multiclass
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                15                 96
  M1                 0                  2
  M1A                0                  3
  MX                 4                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     3  22
  11Q GAIN WILD-TYPE  18 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3   22
  11Q GAIN WILD-TYPE   18  107
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                 18
  MALE                 22                107
[1] 2 2
[1] FALSE
D22V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       6                         0    18
  11Q GAIN WILD-TYPE    32                         2    75
D22V9, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    6                 32
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   18                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   29 14
  12P GAIN WILD-TYPE 59 40
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                43                 99 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                14                 40 
$`12P GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A50L 
        7.63        16.24        20.09         2.63         0.03         0.53 
TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI 
       23.41         0.46         0.30         4.31         3.52         8.78 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A88Y TCGA-L5-A8NF TCGA-L5-A8NL 
        4.08         3.32         4.90         0.36         2.66        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        5.42        21.37        27.12        10.36         0.07        10.45 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10         0.13         0.10         0.07         0.07         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6DN 
        0.10         0.07         0.07         0.20         1.18         8.02 
TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-VR-A8EU TCGA-VR-A8EW 
        7.59        29.59        53.95        14.01        18.31         8.12 
TCGA-VR-A8Q7 
       36.72 

$`12P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
        8.94         4.21        32.45        33.27         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
       20.12         0.26         0.99        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
        0.13        14.86         0.43       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        15.48 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        25.28        18.08        17.59         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.45         8.94         3.68         3.35        19.50         6.41 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
       18.35         7.17         1.38         3.16        30.74        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH 
        7.40         3.95         3.02        55.50        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS 
       13.48        16.47        13.55         7.76         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       83.24        52.57        46.09         0.16         0.07         0.33 
TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A9 
        0.07         0.10         0.07         0.13         0.10         0.07 
TCGA-LN-A4MQ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.10        17.62         5.16         3.78         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        7.04         6.35         9.30         7.00         8.78         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-AA4G 
        3.42         4.80         8.48         8.15         4.44        12.03 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        9.17        15.91        18.12 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.03               0.07 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             53.95             122.10 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              4.08               8.71 
[1] "0.0 - 54.0 (4.1)"  "0.1 - 122.1 (8.7)"
[1] "hr=" "1.3"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P GAIN MUTATED         0        1        1        1        11         6
  12P GAIN WILD-TYPE       8        3        5        0        24        20
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           8          3          3          3        2
  12P GAIN WILD-TYPE        15          8          5          3        1
                    vv
clus                 STAGE IVA
  12P GAIN MUTATED           2
  12P GAIN WILD-TYPE         0
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  1                  3
  STAGE IB                  1                  5
  STAGE II                  1                  0
  STAGE IIA                11                 24
  STAGE IIB                 6                 20
  STAGE III                 8                 15
  STAGE IIIA                3                  8
  STAGE IIIB                3                  5
  STAGE IIIC                3                  3
  STAGE IV                  2                  1
  STAGE IVA                 2                  0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  12P GAIN MUTATED       4 10 28  0
  12P GAIN WILD-TYPE    22 23 46  4
D23V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1                4                 22
  T2                  10                 23
  T3                  28                 46
  T4                   0                  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                 N0 N1 N2 N3
  12P GAIN MUTATED   20 16  3  3
  12P GAIN WILD-TYPE 44 38  8  3
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               20                 44
  N1               16                 38
  N2                3                  8
  N3                3                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  12P GAIN MUTATED   31  1   3  5
  12P GAIN WILD-TYPE 80  1   0 12
D23V6, multiclass
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0                31                 80
  M1                 1                  1
  M1A                3                  0
  MX                 5                 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"
D23V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    3 43
  12P GAIN WILD-TYPE 18 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3   43
  12P GAIN WILD-TYPE   18   86
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                3                 18
  MALE                 43                 86
[1] 2 2
[1] FALSE
D23V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED      19                         0    25
  12P GAIN WILD-TYPE    19                         2    68
D23V9, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                   19                 19
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   25                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED   22  7
  12Q GAIN WILD-TYPE 66 47
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                29                113 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 7                 47 
$`12Q GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A8O2 TCGA-L5-A4OE 
        7.63        16.24         2.63         0.53         0.46         3.52 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A88Y TCGA-L5-A8NL TCGA-L5-A8NN 
        4.08         3.32         4.90         0.36        13.22         5.42 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49V TCGA-LN-A49W 
       27.12        52.57        10.36        10.45         0.10         0.07 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.07         0.07         0.10         0.20         1.18 
TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-ZR-A9CJ 
        7.59        29.59        18.31        36.72        18.12 

$`12Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94         4.21        32.45        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
       20.78        20.12         0.03         0.26         0.99        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
        0.79        23.41         0.36         0.13        14.86         0.43 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
      122.10        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        15.48        23.18        25.28        18.08 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       17.59         6.21         3.16         3.45         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        8.94         3.68         3.35        19.50         8.78         6.41 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
       18.35         7.17         1.38         3.16        30.74        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        7.40         3.95         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ 
       12.92        13.48        16.47        13.55         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M 
        8.71        13.41        83.24        46.09         0.07         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X 
        0.07         0.33         0.10         0.13         0.07         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4MR 
        0.07         0.13         0.07         0.10         0.10         0.07 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 
       17.62         5.16         3.78         8.02         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
        7.04         6.35        53.95         9.30         7.00         8.78 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       14.01         5.29         3.42         4.80         8.48         8.15 
TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        4.44         8.12        12.03         9.17        15.91 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.07               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             52.57             122.10 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              4.08               8.12 
[1] "0.1 - 52.6 (4.1)"  "0.0 - 122.1 (8.1)"
[1] "hr=" "1.2"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED         0        1        0        1         7         2
  12Q GAIN WILD-TYPE       8        3        6        0        28        24
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED           5          3          2          3        2
  12Q GAIN WILD-TYPE        18          8          6          3        1
                    vv
clus                 STAGE IVA
  12Q GAIN MUTATED           1
  12Q GAIN WILD-TYPE         1
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  1                  3
  STAGE IB                  0                  6
  STAGE II                  1                  0
  STAGE IIA                 7                 28
  STAGE IIB                 2                 24
  STAGE III                 5                 18
  STAGE IIIA                3                  8
  STAGE IIIB                2                  6
  STAGE IIIC                3                  3
  STAGE IV                  2                  1
  STAGE IVA                 1                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  12Q GAIN MUTATED       3  6 19  0
  12Q GAIN WILD-TYPE    23 27 55  4
D24V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1                3                 23
  T2                   6                 27
  T3                  19                 55
  T4                   0                  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                 N0 N1 N2 N3
  12Q GAIN MUTATED   11 12  2  3
  12Q GAIN WILD-TYPE 53 42  9  3
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               11                 53
  N1               12                 42
  N2                2                  9
  N3                3                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  12Q GAIN MUTATED   20  1   2  3
  12Q GAIN WILD-TYPE 91  1   1 14
D24V6, multiclass
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0                20                 91
  M1                 1                  1
  M1A                2                  1
  MX                 3                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  28
  12Q GAIN WILD-TYPE  19 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   28
  12Q GAIN WILD-TYPE   19  101
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                2                 19
  MALE                 28                101
[1] 2 2
[1] FALSE
D24V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED      12                         0    16
  12Q GAIN WILD-TYPE    26                         2    77
D24V9, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                   12                 26
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   16                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED   22 14
  13Q GAIN WILD-TYPE 66 40
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                36                106 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                14                 40 
$`13Q GAIN MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IG-A5B8 TCGA-IG-A97H 
       31.27        14.30         5.92        13.94         0.79         0.43 
TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C 
      122.10         3.68        42.77        23.18        25.28         3.16 
TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OP TCGA-L5-A4OQ 
        3.45         8.94         3.35         8.78         7.17         1.38 
TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
        7.13         2.60         0.36         3.02         2.66        12.92 
TCGA-L5-A8NT TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 
       27.12         0.10         1.18         3.78        14.70         7.04 
TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-ZR-A9CJ 
        9.30         8.78         5.29         3.42         8.15        18.12 

$`13Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        58.55         7.63         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12         0.03         0.26         0.99         0.53        17.03 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA 
       23.41         0.36         0.13        14.86         0.46        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93E 
       60.39        68.02        41.52        25.41        15.48        18.08 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF 
       17.59         6.21         0.30         4.31         3.52         3.68 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR 
       19.50         6.41         4.08        18.35         3.32         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
       30.74         4.90        29.00         7.43         6.94         8.71 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NI 
       25.12         7.40         3.95        55.50        35.97        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.42        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        13.41        83.24        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
        0.07        10.45         0.16         0.07         0.33         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.13         0.07         0.10         0.07         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.13         0.07         0.10         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN 
        0.07         0.07         0.20        17.62         5.16         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-RE-A7BO 
        7.59         5.06        29.59         6.35        53.95         7.00 
TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW 
       14.01         4.80         8.48         4.44        18.31         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       36.72        12.03         9.17        15.91 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.10               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            122.10              83.24 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             7.085              7.695 
[1] "0.1 - 122.1 (7.1)" "0.0 - 83.2 (7.7)" 
[1] "hr=" "1.2"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q GAIN MUTATED         4        1        1        0         3         5
  13Q GAIN WILD-TYPE       4        3        5        1        32        21
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED           5          2          2          3        1
  13Q GAIN WILD-TYPE        18          9          6          3        2
                    vv
clus                 STAGE IVA
  13Q GAIN MUTATED           1
  13Q GAIN WILD-TYPE         1
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  1                  3
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 3                 32
  STAGE IIB                 5                 21
  STAGE III                 5                 18
  STAGE IIIA                2                  9
  STAGE IIIB                2                  6
  STAGE IIIC                3                  3
  STAGE IV                  1                  2
  STAGE IVA                 1                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  13Q GAIN MUTATED      11  6 14  0
  13Q GAIN WILD-TYPE    15 27 60  4
D25V4, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1               11                 15
  T2                   6                 27
  T3                  14                 60
  T4                   0                  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                 N0 N1 N2 N3
  13Q GAIN MUTATED   12 11  4  3
  13Q GAIN WILD-TYPE 52 43  7  3
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               12                 52
  N1               11                 43
  N2                4                  7
  N3                3                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  13Q GAIN MUTATED   20  1   1  9
  13Q GAIN WILD-TYPE 91  1   2  8
D25V6, multiclass
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0                20                 91
  M1                 1                  1
  M1A                1                  2
  MX                 9                  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"
D25V7, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    5 32
  13Q GAIN WILD-TYPE 16 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5   32
  13Q GAIN WILD-TYPE   16   97
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                5                 16
  MALE                 32                 97
[1] 2 2
[1] FALSE
D25V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       5                         1    24
  13Q GAIN WILD-TYPE    33                         1    69
D25V9, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    5                 33
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   24                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED   21 13
  14Q GAIN WILD-TYPE 67 41
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                34                108 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                13                 41 
$`14Q GAIN MUTATED`
TCGA-2H-A9GL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A6QS TCGA-JY-A93C 
        5.92         0.85        20.78         0.03         0.13        23.18 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OR TCGA-L5-A4OX TCGA-L5-A8NG 
        3.16         3.45         4.31         3.16         7.43        35.97 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49U 
        5.42        21.37        13.41         0.07         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10         0.10         0.10         0.07         0.07         0.20 
TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6Y0 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-AASX 
        1.18         8.02        53.95         8.78        14.01         4.44 
TCGA-VR-A8EW TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        8.12         9.17        15.91        18.12 

$`14Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        20.09 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12         0.26         0.99         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41         0.36        14.86         0.46         0.43 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
      122.10        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       42.77        25.41        15.48        25.28        18.08        17.59 
TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        6.21         0.30         8.94         3.52         3.68         3.35 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       19.50         8.78         6.41         4.08        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38        30.74         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        6.94         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.95         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NT 
       16.47        13.55        13.22         7.76         8.71        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       83.24        52.57        46.09        10.36        10.45         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 
        0.07         0.33         0.10         0.07         0.07         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-M9-A5M8 
        0.07         0.10         0.10         0.07         0.10        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         3.78         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC 
       29.59         6.35         9.30         7.00         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G 
        4.80         8.48         8.15        18.31        36.72        12.03 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.03               0.07 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             53.95             122.10 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             4.375              8.315 
[1] "0.0 - 54.0 (4.4)"  "0.1 - 122.1 (8.3)"
[1] "hr=" "1.6"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         1        1        1        0        12         6
  14Q GAIN WILD-TYPE       7        3        5        1        23        20
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED           6          3          2          2        0
  14Q GAIN WILD-TYPE        17          8          6          4        3
                    vv
clus                 STAGE IVA
  14Q GAIN MUTATED           0
  14Q GAIN WILD-TYPE         2
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  1                  3
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                12                 23
  STAGE IIB                 6                 20
  STAGE III                 6                 17
  STAGE IIIA                3                  8
  STAGE IIIB                2                  6
  STAGE IIIC                2                  4
  STAGE IV                  0                  3
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  14Q GAIN MUTATED       2 11 18  3
  14Q GAIN WILD-TYPE    24 22 56  1
D26V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1                2                 24
  T2                  11                 22
  T3                  18                 56
  T4                   3                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  14Q GAIN MUTATED   20 10  2  2
  14Q GAIN WILD-TYPE 44 44  9  4
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               20                 44
  N1               10                 44
  N2                2                  9
  N3                2                  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                 M0 M1 M1A MX
  14Q GAIN MUTATED   29  0   0  5
  14Q GAIN WILD-TYPE 82  2   3 12
D26V6, multiclass
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                29                 82
  M1                 0                  2
  M1A                0                  3
  MX                 5                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    0 38
  14Q GAIN WILD-TYPE 21 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   38
  14Q GAIN WILD-TYPE   21   91
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                0                 21
  MALE                 38                 91
[1] 2 2
[1] FALSE
D26V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED      15                         0    21
  14Q GAIN WILD-TYPE    23                         2    72
D26V9, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                   15                 23
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   21                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED   12 10
  15Q GAIN WILD-TYPE 76 44
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                22                120 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                 44 
$`15Q GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-IG-A50L TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-L5-A43C 
        7.63         8.94         0.53       122.10        60.39         3.16 
TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NJ 
        3.16         7.13         6.94         2.60         0.36        16.47 
TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A4MR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       46.09        10.45         0.10         0.07        17.62         3.78 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-VR-AA7D 
        7.59         7.04         6.35         9.17 

$`15Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12         0.03         0.26         0.99 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41         0.36         0.13        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        0.46         0.43        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        15.48        23.18        25.28        18.08 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       17.59         6.21         3.45         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.52         3.68         3.35        19.50         8.78         6.41 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
        4.08        18.35         3.32         7.17         1.38        30.74 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
        4.90        29.00         7.43         8.71        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        13.55        13.22         7.76         5.42        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ 
        8.71        13.41        27.12        83.24        52.57        10.36 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
        0.07         0.16         0.07         0.33         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10         0.07         0.10         0.07         0.13         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10         0.10         0.10         0.07         0.07         0.10 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.20         1.18         5.16         8.02         5.06        14.70 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
       29.59        53.95         9.30         7.00         8.78        14.01 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42         4.80         8.48         8.15         4.44 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7I TCGA-ZR-A9CJ 
       18.31         8.12        36.72        12.03        15.91        18.12 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.07               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            122.10              83.24 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             7.085              7.890 
[1] "0.1 - 122.1 (7.1)" "0.0 - 83.2 (7.9)" 
[1] "hr=" "1.2"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q GAIN MUTATED         2        1        2        0         5         1
  15Q GAIN WILD-TYPE       6        3        4        1        30        25
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           5          1          1          1        0
  15Q GAIN WILD-TYPE        18         10          7          5        3
                    vv
clus                 STAGE IVA
  15Q GAIN MUTATED           0
  15Q GAIN WILD-TYPE         2
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  1                  3
  STAGE IB                  2                  4
  STAGE II                  0                  1
  STAGE IIA                 5                 30
  STAGE IIB                 1                 25
  STAGE III                 5                 18
  STAGE IIIA                1                 10
  STAGE IIIB                1                  7
  STAGE IIIC                1                  5
  STAGE IV                  0                  3
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  15Q GAIN MUTATED       4  6 10  0
  15Q GAIN WILD-TYPE    22 27 64  4
D27V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1                4                 22
  T2                   6                 27
  T3                  10                 64
  T4                   0                  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                 N0 N1 N2 N3
  15Q GAIN MUTATED   10  8  1  1
  15Q GAIN WILD-TYPE 54 46 10  5
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               10                 54
  N1                8                 46
  N2                1                 10
  N3                1                  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                 M0 M1 M1A MX
  15Q GAIN MUTATED   16  0   0  4
  15Q GAIN WILD-TYPE 95  2   3 13
D27V6, multiclass
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                16                 95
  M1                 0                  2
  M1A                0                  3
  MX                 4                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     2  22
  15Q GAIN WILD-TYPE  19 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2   22
  15Q GAIN WILD-TYPE   19  107
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                2                 19
  MALE                 22                107
[1] 2 2
[1] FALSE
D27V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       6                         0    13
  15Q GAIN WILD-TYPE    32                         2    80
D27V9, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    6                 32
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   13                 80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED   21  9
  16P GAIN WILD-TYPE 67 45
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                30                112 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 9                 45 
$`16P GAIN MUTATED`
TCGA-2H-A9GJ TCGA-IG-A3Y9 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A8O2 TCGA-IG-A97H 
       58.55         0.85         0.53         0.79         0.46         0.43 
TCGA-L5-A43H TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NE TCGA-L5-A8NF 
        0.30         3.32        29.00         6.94        55.50         2.66 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49S 
       21.37        13.41        27.12        10.36         0.07         0.13 
TCGA-LN-A49W TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U6 
        0.07         0.07         0.10         0.10         0.07         0.20 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EW TCGA-ZR-A9CJ 
        5.06        29.59        14.01         8.48         8.12        18.12 

$`16P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        20.09 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12         0.03         0.26         0.99 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 
       17.03        23.41         0.36         0.13        14.86       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        15.48        23.18        25.28        18.08        17.59 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
        6.21         3.16         3.45         4.31         8.94         3.52 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.68         3.35        19.50         8.78         6.41         4.08 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         7.17         1.38         3.16        30.74         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.13         7.43         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.95         3.02        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR 
       16.47        13.55        13.22         7.76         5.42         8.71 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       83.24        52.57        46.09        10.45         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
        0.33         0.10         0.07         0.10         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 
        0.13         0.10         0.07         0.10         0.07         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       17.62         5.16         3.78         8.02         7.59        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
        7.04         6.35        53.95         9.30         7.00         8.78 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU 
        5.29         3.42         4.80         8.15         4.44        18.31 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       36.72        12.03         9.17        15.91 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.07               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             58.55             122.10 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              2.99               7.89 
[1] "0.1 - 58.5 (3.0)"  "0.0 - 122.1 (7.9)"
[1] "hr=" "1"  
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED         1        0        3        1         7         5
  16P GAIN WILD-TYPE       7        4        3        0        28        21
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           5          2          2          3        0
  16P GAIN WILD-TYPE        18          9          6          3        3
                    vv
clus                 STAGE IVA
  16P GAIN MUTATED           1
  16P GAIN WILD-TYPE         1
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  0                  4
  STAGE IB                  3                  3
  STAGE II                  1                  0
  STAGE IIA                 7                 28
  STAGE IIB                 5                 21
  STAGE III                 5                 18
  STAGE IIIA                2                  9
  STAGE IIIB                2                  6
  STAGE IIIC                3                  3
  STAGE IV                  0                  3
  STAGE IVA                 1                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  16P GAIN MUTATED       2  6 21  1
  16P GAIN WILD-TYPE    24 27 53  3
D28V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1                2                 24
  T2                   6                 27
  T3                  21                 53
  T4                   1                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  16P GAIN MUTATED   16  8  2  3
  16P GAIN WILD-TYPE 48 46  9  3
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               16                 48
  N1                8                 46
  N2                2                  9
  N3                3                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  16P GAIN MUTATED   24  0   1  5
  16P GAIN WILD-TYPE 87  2   2 12
D28V6, multiclass
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                24                 87
  M1                 0                  2
  M1A                1                  2
  MX                 5                 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"
D28V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    0 32
  16P GAIN WILD-TYPE 21 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   32
  16P GAIN WILD-TYPE   21   97
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                0                 21
  MALE                 32                 97
[1] 2 2
[1] FALSE
D28V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED      14                         1    16
  16P GAIN WILD-TYPE    24                         1    77
D28V9, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                   14                 24
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   16                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   16 10
  16Q GAIN WILD-TYPE 72 44
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                26                116 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                10                 44 
$`16Q GAIN MUTATED`
TCGA-2H-A9GM TCGA-IG-A3Y9 TCGA-IG-A5B8 TCGA-IG-A8O2 TCGA-L5-A43H TCGA-L5-A43J 
       13.94         0.85         0.79         0.46         0.30         4.31 
TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NF TCGA-L5-A8NQ TCGA-L5-A8NS 
        3.32        29.00         6.94         2.66        21.37        13.41 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-LN-A49R TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
       27.12        52.57         0.10         0.07         0.10         0.10 
TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-R6-A6XG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV 
        0.07         0.20        29.59        14.01         3.42         8.48 
TCGA-VR-A8EW TCGA-ZR-A9CJ 
        8.12        18.12 

$`16Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        20.09 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12         0.03         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03        23.41         0.36         0.13        14.86 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        0.43       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        15.48        23.18        25.28 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M 
       18.08        17.59         6.21         3.16         3.45         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.52         3.68         3.35        19.50         8.78         6.41 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        4.08        18.35         7.17         1.38         3.16        30.74 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        4.90         7.13         7.43         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG 
        0.36         7.40         3.95         3.02        55.50        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
        5.42         8.71        83.24        46.09        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       10.45         0.16         0.07         0.33         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 
        0.10         0.07         0.10         0.07         0.13         0.10 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.07         0.10         0.07         1.18        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        3.78         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        6.35        53.95         9.30         7.00         8.78         5.29 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G 
        4.80         8.15         4.44        18.31        36.72        12.03 
TCGA-VR-AA7D TCGA-VR-AA7I 
        9.17        15.91 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.07               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             52.57             122.10 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             3.865              7.695 
[1] "0.1 - 52.6 (3.9)"  "0.0 - 122.1 (7.7)"
[1] "hr=" "1.4"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED         0        0        3        1         5         6
  16Q GAIN WILD-TYPE       8        4        3        0        30        20
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED           5          1          2          2        0
  16Q GAIN WILD-TYPE        18         10          6          4        3
                    vv
clus                 STAGE IVA
  16Q GAIN MUTATED           1
  16Q GAIN WILD-TYPE         1
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  0                  4
  STAGE IB                  3                  3
  STAGE II                  1                  0
  STAGE IIA                 5                 30
  STAGE IIB                 6                 20
  STAGE III                 5                 18
  STAGE IIIA                1                 10
  STAGE IIIB                2                  6
  STAGE IIIC                2                  4
  STAGE IV                  0                  3
  STAGE IVA                 1                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  16Q GAIN MUTATED       2  5 18  1
  16Q GAIN WILD-TYPE    24 28 56  3
D29V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1                2                 24
  T2                   5                 28
  T3                  18                 56
  T4                   1                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  16Q GAIN MUTATED   15  7  2  2
  16Q GAIN WILD-TYPE 49 47  9  4
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               15                 49
  N1                7                 47
  N2                2                  9
  N3                2                  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                 M0 M1 M1A MX
  16Q GAIN MUTATED   20  0   1  5
  16Q GAIN WILD-TYPE 91  2   2 12
D29V6, multiclass
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                20                 91
  M1                 0                  2
  M1A                1                  2
  MX                 5                 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"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0  28
  16Q GAIN WILD-TYPE  21 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   28
  16Q GAIN WILD-TYPE   21  101
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                0                 21
  MALE                 28                101
[1] 2 2
[1] FALSE
D29V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED      10                         2    15
  16Q GAIN WILD-TYPE    28                         0    78
D29V9, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                   10                 28
  BLACK OR AFRICAN AMERICAN                2                  0
  WHITE                                   15                 78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED   14  9
  17P GAIN WILD-TYPE 74 45
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                23                119 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 9                 45 
$`17P GAIN MUTATED`
TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A51D TCGA-JY-A6FB TCGA-JY-A93C TCGA-JY-A93E 
       20.09         0.53        17.03        60.39        23.18        18.08 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A88Z TCGA-L5-A8NE 
        0.30         4.31        18.35         1.38         7.40        55.50 
TCGA-L5-A8NG TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A4 
       35.97         0.33         0.10         0.10         0.13         0.10 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-V5-A7RC TCGA-VR-A8EU TCGA-VR-AA7I 
        8.02         5.06         3.42        18.31        15.91 

$`17P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12         0.03         0.26 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.99         0.79        23.41         0.36         0.13        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        0.46         0.43       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F 
       41.52        42.77        25.41        15.48        25.28        17.59 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        6.21         3.16         3.45         8.94         3.52         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO 
        3.35        19.50         8.78         6.41         4.08         3.32 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         3.16        30.74         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.43         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.95         3.02         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.42        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.41        27.12        83.24        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49U 
        0.07        10.45         0.16         0.07         0.13         0.07 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.07         0.10         0.07         0.07         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.07         0.07         0.10         0.07         0.20         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       17.62         5.16         3.78         7.59        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
       29.59         6.35        53.95         9.30         7.00         8.78 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       14.01         5.29         4.80         8.48         8.15         4.44 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-ZR-A9CJ 
        8.12        36.72        12.03         9.17        18.12 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.10               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             60.39             122.10 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              7.40               7.59 
[1] "0.1 - 60.4 (7.4)"  "0.0 - 122.1 (7.6)"
[1] "hr=" "1"  
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         1        0        0        0         5         5
  17P GAIN WILD-TYPE       7        4        6        1        30        21
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED           5          3          1          0        1
  17P GAIN WILD-TYPE        18          8          7          6        2
                    vv
clus                 STAGE IVA
  17P GAIN MUTATED           0
  17P GAIN WILD-TYPE         2
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  0                  4
  STAGE IB                  0                  6
  STAGE II                  0                  1
  STAGE IIA                 5                 30
  STAGE IIB                 5                 21
  STAGE III                 5                 18
  STAGE IIIA                3                  8
  STAGE IIIB                1                  7
  STAGE IIIC                0                  6
  STAGE IV                  1                  2
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  17P GAIN MUTATED       5  3 12  1
  17P GAIN WILD-TYPE    21 30 62  3
D30V4, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1                5                 21
  T2                   3                 30
  T3                  12                 62
  T4                   1                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  17P GAIN MUTATED    8 11  2  0
  17P GAIN WILD-TYPE 56 43  9  6
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                8                 56
  N1               11                 43
  N2                2                  9
  N3                0                  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                 M0 M1 M1A MX
  17P GAIN MUTATED   17  1   0  2
  17P GAIN WILD-TYPE 94  1   3 15
D30V6, multiclass
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                17                 94
  M1                 1                  1
  M1A                0                  3
  MX                 2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     1  23
  17P GAIN WILD-TYPE  20 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   23
  17P GAIN WILD-TYPE   20  106
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                1                 20
  MALE                 23                106
[1] 2 2
[1] FALSE
D30V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       8                         1    15
  17P GAIN WILD-TYPE    30                         1    78
D30V9, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    8                 30
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   15                 78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED   24 11
  17Q GAIN WILD-TYPE 64 43
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                35                107 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                11                 43 
$`17Q GAIN MUTATED`
TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-JY-A6FB TCGA-JY-A93C 
       20.09         0.53        17.03         0.36        60.39        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4ON 
       25.28        18.08         3.45         0.30         3.52        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NG 
        3.32         1.38         4.90         7.40        55.50        35.97 
TCGA-L5-A8NN TCGA-L5-A8NT TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A2 
        5.42        27.12         0.10         0.13         0.10         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG 
        0.07         0.10         8.02         7.59         5.06        29.59 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-AA7I 
        3.42         8.48         8.15        18.31        15.91 

$`17Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12         0.03         0.26 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.99         0.79        23.41         0.13        14.86         0.46 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        0.43       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       42.77        25.41        15.48        17.59         6.21         3.16 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        4.31         8.94         3.68         3.35        19.50         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
        6.41         4.08         7.17         3.16        30.74        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        0.36         3.95         3.02         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        83.24        52.57        46.09        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49W 
       10.45         0.16         0.07         0.33         0.07         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.10         0.07         0.10         0.10         0.07         0.07 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.10         0.07         0.20         1.18        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        3.78        14.70         7.04         6.35        53.95         9.30 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASX 
        7.00         8.78        14.01         5.29         4.80         4.44 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-ZR-A9CJ 
        8.12        36.72        12.03         9.17        18.12 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.07               0.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             60.39             122.10 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              7.40               7.63 
[1] "0.1 - 60.4 (7.4)"  "0.0 - 122.1 (7.6)"
[1] "hr=" "1.2"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED         2        0        0        0         5         6
  17Q GAIN WILD-TYPE       6        4        6        1        30        20
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED           7          3          3          2        2
  17Q GAIN WILD-TYPE        16          8          5          4        1
                    vv
clus                 STAGE IVA
  17Q GAIN MUTATED           0
  17Q GAIN WILD-TYPE         2
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  0                  4
  STAGE IB                  0                  6
  STAGE II                  0                  1
  STAGE IIA                 5                 30
  STAGE IIB                 6                 20
  STAGE III                 7                 16
  STAGE IIIA                3                  8
  STAGE IIIB                3                  5
  STAGE IIIC                2                  4
  STAGE IV                  2                  1
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  17Q GAIN MUTATED       6  4 19  1
  17Q GAIN WILD-TYPE    20 29 55  3
D31V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1                6                 20
  T2                   4                 29
  T3                  19                 55
  T4                   1                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  17Q GAIN MUTATED   10 14  4  2
  17Q GAIN WILD-TYPE 54 40  7  4
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               10                 54
  N1               14                 40
  N2                4                  7
  N3                2                  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                 M0 M1 M1A MX
  17Q GAIN MUTATED   24  1   1  2
  17Q GAIN WILD-TYPE 87  1   2 15
D31V6, multiclass
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0                24                 87
  M1                 1                  1
  M1A                1                  2
  MX                 2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    2 34
  17Q GAIN WILD-TYPE 19 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2   34
  17Q GAIN WILD-TYPE   19   95
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                2                 19
  MALE                 34                 95
[1] 2 2
[1] FALSE
D31V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED      10                         2    24
  17Q GAIN WILD-TYPE    28                         0    69
D31V9, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                   10                 28
  BLACK OR AFRICAN AMERICAN                2                  0
  WHITE                                   24                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED   23 17
  18P GAIN WILD-TYPE 65 37
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                40                102 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                17                 37 
$`18P GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A50L TCGA-IG-A625 TCGA-JY-A6FB 
        7.63        13.94         4.21         0.53         0.36        60.39 
TCGA-JY-A6FE TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
        3.68        25.41         4.31         4.08        18.35         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A8NL TCGA-L5-A8NN 
        3.16         4.90         7.13         0.36        13.22         5.42 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49S 
       21.37        13.41        27.12        83.24        46.09         0.13 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.07         0.10         0.07         0.10         0.07         0.10 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6KZ TCGA-S8-A6BW 
        0.10         0.07         0.20         1.18         5.06        14.01 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8Q7 TCGA-VR-AA7I 
        3.42         4.80        36.72        15.91 

$`18P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        14.30        58.55         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       16.24        32.45        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        2.63        20.12         0.03         0.26         0.99        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41         0.13        14.86         0.46         0.43 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75        68.02        41.52        42.77        15.48 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        25.28        18.08        17.59         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.45         0.30         8.94         3.52         3.68         3.35 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS 
       19.50         8.78         6.41         3.32         7.17        30.74 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        7.40         3.95         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NR 
       12.92        13.48        16.47        13.55         7.76         8.71 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       52.57        10.36         0.07        10.45         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.33         0.10         0.07         0.13         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.07         0.07        17.62         5.16         3.78         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW 
        9.30         7.00         8.78         5.29         8.48         8.15 
TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D TCGA-ZR-A9CJ 
        4.44        18.31         8.12        12.03         9.17        18.12 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.07               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             83.24             122.10 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             4.260              8.595 
[1] "0.1 - 83.2 (4.3)"  "0.0 - 122.1 (8.6)"
[1] "hr=" "1.5"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED         1        2        3        0         9         8
  18P GAIN WILD-TYPE       7        2        3        1        26        18
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED          10          3          1          0        1
  18P GAIN WILD-TYPE        13          8          7          6        2
                    vv
clus                 STAGE IVA
  18P GAIN MUTATED           0
  18P GAIN WILD-TYPE         2
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  2                  2
  STAGE IB                  3                  3
  STAGE II                  0                  1
  STAGE IIA                 9                 26
  STAGE IIB                 8                 18
  STAGE III                10                 13
  STAGE IIIA                3                  8
  STAGE IIIB                1                  7
  STAGE IIIC                0                  6
  STAGE IV                  1                  2
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  18P GAIN MUTATED       7 10 21  1
  18P GAIN WILD-TYPE    19 23 53  3
D32V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1                7                 19
  T2                  10                 23
  T3                  21                 53
  T4                   1                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  18P GAIN MUTATED   20 17  2  0
  18P GAIN WILD-TYPE 44 37  9  6
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               20                 44
  N1               17                 37
  N2                2                  9
  N3                0                  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                 M0 M1 M1A MX
  18P GAIN MUTATED   31  0   1  5
  18P GAIN WILD-TYPE 80  2   2 12
D32V6, multiclass
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                31                 80
  M1                 0                  2
  M1A                1                  2
  MX                 5                 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"
D32V7, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    2 39
  18P GAIN WILD-TYPE 19 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   39
  18P GAIN WILD-TYPE   19   90
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                2                 19
  MALE                 39                 90
[1] 2 2
[1] FALSE
D32V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED      13                         1    23
  18P GAIN WILD-TYPE    25                         1    70
D32V9, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                   13                 25
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   23                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED   10 11
  18Q GAIN WILD-TYPE 78 43
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                21                121 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                11                 43 
$`18Q GAIN MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A625 
        7.63         5.92        13.94         4.21        33.27         0.36 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-L5-A43E TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88Y 
       60.39         3.68         3.45         3.16         7.13         0.36 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-LN-A49X TCGA-LN-A4A3 TCGA-R6-A6KZ 
       13.22         5.42        21.37         0.10         0.07         5.06 
TCGA-S8-A6BW TCGA-VR-A8Q7 TCGA-VR-AA7I 
       14.01        36.72        15.91 

$`18Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        14.30        58.55         8.94        16.24 
TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       32.45        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
        0.03         0.26         0.99         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
       23.41         0.13        14.86         0.46         0.43       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       44.75        68.02        41.52        42.77        25.41        15.48 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        25.28        18.08        17.59         6.21         3.16 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        0.30         4.31         8.94         3.52         3.68         3.35 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       19.50         8.78         6.41         4.08        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        7.17         1.38        30.74         4.90        29.00         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        6.94         8.71         2.60        25.12         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.02        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       16.47        13.55         7.76         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        46.09        10.36         0.07        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        0.16         0.07         0.33         0.10         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10         0.07         0.07         0.13         0.10         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10         0.07         0.07         0.10         0.07         0.20 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        1.18        17.62         5.16         3.78         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00         8.78         5.29         3.42         4.80         8.48 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D 
        8.15         4.44        18.31         8.12        12.03         9.17 
TCGA-ZR-A9CJ 
       18.12 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.07               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             60.39             122.10 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              5.92               7.76 
[1] "0.1 - 60.4 (5.9)"  "0.0 - 122.1 (7.8)"
[1] "hr=" "1.6"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         2        1        1        0         3         2
  18Q GAIN WILD-TYPE       6        3        5        1        32        24
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED           9          1          1          0        0
  18Q GAIN WILD-TYPE        14         10          7          6        3
                    vv
clus                 STAGE IVA
  18Q GAIN MUTATED           0
  18Q GAIN WILD-TYPE         2
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  1                  3
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 3                 32
  STAGE IIB                 2                 24
  STAGE III                 9                 14
  STAGE IIIA                1                 10
  STAGE IIIB                1                  7
  STAGE IIIC                0                  6
  STAGE IV                  0                  3
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  18Q GAIN MUTATED       5  3 12  1
  18Q GAIN WILD-TYPE    21 30 62  3
D33V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1                5                 21
  T2                   3                 30
  T3                  12                 62
  T4                   1                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  18Q GAIN MUTATED    9 11  1  0
  18Q GAIN WILD-TYPE 55 43 10  6
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                9                 55
  N1               11                 43
  N2                1                 10
  N3                0                  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                 M0 M1 M1A MX
  18Q GAIN MUTATED   18  0   0  3
  18Q GAIN WILD-TYPE 93  2   3 14
D33V6, multiclass
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                18                 93
  M1                 0                  2
  M1A                0                  3
  MX                 3                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2  20
  18Q GAIN WILD-TYPE  19 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   20
  18Q GAIN WILD-TYPE   19  109
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                2                 19
  MALE                 20                109
[1] 2 2
[1] FALSE
D33V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       4                         0    13
  18Q GAIN WILD-TYPE    34                         2    80
D33V9, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    4                 34
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   13                 80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED   13  7
  19P GAIN WILD-TYPE 75 47
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                20                122 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 7                 47 
$`19P GAIN MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-IG-A3QL TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OO 
       58.55         8.94        20.09         3.16         3.52         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A8NG TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49K 
        1.38         3.16        35.97        27.12        10.36         0.07 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A5U7 TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-S8-A6BW 
        0.13         0.10         1.18         5.06        29.59        14.01 
TCGA-V5-AASV TCGA-VR-AA7I 
        8.48        15.91 

$`19P GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
       16.24         4.21        32.45        33.27         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12         0.03         0.26         0.99         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41         0.36         0.13        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.46         0.43       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.68        41.52        42.77        25.41        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       25.28        18.08        17.59         6.21         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        4.31         8.94         3.68         3.35        19.50         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT 
        6.41         4.08        18.35         7.17        30.74         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.42        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       52.57        46.09        10.45         0.16         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        0.10         0.07         0.07         0.10         0.07         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.07         0.10         0.10         0.10         0.07         0.07 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.10         0.07         0.20        17.62         5.16         3.78 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        8.02         7.59        14.70         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        9.30         7.00         8.78         5.29         3.42         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.15         4.44        18.31         8.12        36.72        12.03 
TCGA-VR-AA7D TCGA-ZR-A9CJ 
        9.17        18.12 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.07               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             58.55             122.10 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              6.77               7.51 
[1] "0.1 - 58.5 (6.8)"  "0.0 - 122.1 (7.5)"
[1] "hr=" "1"  
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED         1        1        1        0         5         3
  19P GAIN WILD-TYPE       7        3        5        1        30        23
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           3          1          1          2        0
  19P GAIN WILD-TYPE        20         10          7          4        3
                    vv
clus                 STAGE IVA
  19P GAIN MUTATED           0
  19P GAIN WILD-TYPE         2
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  1                  3
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 5                 30
  STAGE IIB                 3                 23
  STAGE III                 3                 20
  STAGE IIIA                1                 10
  STAGE IIIB                1                  7
  STAGE IIIC                2                  4
  STAGE IV                  0                  3
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  19P GAIN MUTATED       2  4 11  1
  19P GAIN WILD-TYPE    24 29 63  3
D34V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1                2                 24
  T2                   4                 29
  T3                  11                 63
  T4                   1                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  19P GAIN MUTATED   12  2  2  2
  19P GAIN WILD-TYPE 52 52  9  4
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               12                 52
  N1                2                 52
  N2                2                  9
  N3                2                  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                 M0 M1 M1A MX
  19P GAIN MUTATED   12  0   0  5
  19P GAIN WILD-TYPE 99  2   3 12
D34V6, multiclass
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                12                 99
  M1                 0                  2
  M1A                0                  3
  MX                 5                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0  21
  19P GAIN WILD-TYPE  21 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   21
  19P GAIN WILD-TYPE   21  108
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                0                 21
  MALE                 21                108
[1] 2 2
[1] FALSE
D34V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       5                         1    13
  19P GAIN WILD-TYPE    33                         1    80
D34V9, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    5                 33
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   13                 80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   18 12
  19Q GAIN WILD-TYPE 70 42
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                30                112 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                12                 42 
$`19Q GAIN MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A3QL TCGA-IG-A4QS 
       58.55         7.63         8.94        16.24        20.09         0.26 
TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OQ 
        3.16         3.52         3.68        19.50         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A8NG TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV 
        3.16        35.97        13.55         5.42        27.12        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49U TCGA-LN-A4A6 TCGA-LN-A5U7 
       46.09        10.36         0.07         0.07         0.10         1.18 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-AA7I 
        5.06        14.70        29.59        14.01         8.48        15.91 

$`19Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ 
       25.78        31.27        14.30         5.92        13.94         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       32.45        33.27         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        0.03         0.99         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
        0.36         0.13        14.86         0.46         0.43       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        15.48        23.18        25.28        18.08        17.59 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG 
        6.21         3.45         0.30         4.31         8.94         3.35 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OS 
        8.78         6.41         4.08        18.35         7.17        30.74 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        4.90        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        2.60        25.12         0.36         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
       55.50         2.66        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L 
        7.76        21.37         8.71        13.41        83.24        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V 
        0.16         0.07         0.33         0.10         0.13         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.07         0.10         0.07         0.13         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10         0.07         0.07         0.10         0.07         0.20 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 
       17.62         5.16         3.78         8.02         7.59         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        6.35        53.95         9.30         7.00         8.78         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW 
        3.42         4.80         8.15         4.44        18.31         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-ZR-A9CJ 
       36.72        12.03         9.17        18.12 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.07               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             58.55             122.10 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             8.710              7.285 
[1] "0.1 - 58.5 (8.7)"  "0.0 - 122.1 (7.3)"
[1] "hr=" "1"  
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED         2        1        2        1         6         4
  19Q GAIN WILD-TYPE       6        3        4        0        29        22
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           5          1          2          2        0
  19Q GAIN WILD-TYPE        18         10          6          4        3
                    vv
clus                 STAGE IVA
  19Q GAIN MUTATED           1
  19Q GAIN WILD-TYPE         1
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  1                  3
  STAGE IB                  2                  4
  STAGE II                  1                  0
  STAGE IIA                 6                 29
  STAGE IIB                 4                 22
  STAGE III                 5                 18
  STAGE IIIA                1                 10
  STAGE IIIB                2                  6
  STAGE IIIC                2                  4
  STAGE IV                  0                  3
  STAGE IVA                 1                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  19Q GAIN MUTATED       4  6 16  1
  19Q GAIN WILD-TYPE    22 27 58  3
D35V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1                4                 22
  T2                   6                 27
  T3                  16                 58
  T4                   1                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  19Q GAIN MUTATED   15  7  3  2
  19Q GAIN WILD-TYPE 49 47  8  4
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               15                 49
  N1                7                 47
  N2                3                  8
  N3                2                  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                 M0 M1 M1A MX
  19Q GAIN MUTATED   19  0   1  5
  19Q GAIN WILD-TYPE 92  2   2 12
D35V6, multiclass
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0                19                 92
  M1                 0                  2
  M1A                1                  2
  MX                 5                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    1 30
  19Q GAIN WILD-TYPE 20 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   30
  19Q GAIN WILD-TYPE   20   99
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                1                 20
  MALE                 30                 99
[1] 2 2
[1] FALSE
D35V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       5                         1    21
  19Q GAIN WILD-TYPE    33                         1    72
D35V9, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    5                 33
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   21                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   50 34
  20P GAIN WILD-TYPE 38 20
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                84                 58 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                34                 20 
$`20P GAIN MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB 
        4.21        32.45        33.27        20.09         0.85         2.63 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A8O2 
       20.12         0.26         0.53        17.03        23.41         0.46 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        0.43       122.10         3.68        15.48        23.18        25.28 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE 
       18.08         3.16         3.45         0.30         4.31         3.52 
TCGA-L5-A4OG TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
        3.35         4.08        18.35         7.17         1.38        30.74 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43         6.94         2.60 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        0.36         7.40        55.50         2.66        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV 
       16.47         5.42         8.71        13.41        27.12        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49X 
       46.09        10.36        10.45         0.10         0.13         0.10 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.13         0.07         0.10         0.07         0.20         1.18 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        8.02         7.59         5.06        14.70         7.04         6.35 
TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
        9.30         8.78         5.29         3.42         4.80         8.15 
TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        4.44         8.12        36.72         9.17        15.91        18.12 

$`20P GAIN WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT 
       14.30        58.55         7.63        20.78         0.03         0.99 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FB 
        0.79         0.36         0.13        14.86        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93F TCGA-KH-A6WC 
       68.02        41.52        42.77        25.41        17.59         6.21 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO 
        8.94         3.68        19.50         8.78         6.41         3.32 
TCGA-L5-A4OR TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NI 
        3.16         8.71        25.12         3.95         3.02        13.48 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49K 
       13.55        13.22         7.76        21.37        83.24         0.07 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
        0.16         0.07         0.33         0.07         0.10         0.07 
TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.07         0.10         0.10         0.07         0.10         0.07 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-RE-A7BO 
       17.62         5.16         3.78        29.59        53.95         7.00 
TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-AA4G 
       14.01         8.48        18.31        12.03 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.07               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            122.10              83.24 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             7.415              7.695 
[1] "0.1 - 122.1 (7.4)" "0.0 - 83.2 (7.7)" 
[1] "hr=" "1.3"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED         3        2        3        1        16        15
  20P GAIN WILD-TYPE       5        2        3        0        19        11
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED          14          8          5          4        2
  20P GAIN WILD-TYPE         9          3          3          2        1
                    vv
clus                 STAGE IVA
  20P GAIN MUTATED           2
  20P GAIN WILD-TYPE         0
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  2                  2
  STAGE IB                  3                  3
  STAGE II                  1                  0
  STAGE IIA                16                 19
  STAGE IIB                15                 11
  STAGE III                14                  9
  STAGE IIIA                8                  3
  STAGE IIIB                5                  3
  STAGE IIIC                4                  2
  STAGE IV                  2                  1
  STAGE IVA                 2                  0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  20P GAIN MUTATED      16 15 44  2
  20P GAIN WILD-TYPE    10 18 30  2
D36V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1               16                 10
  T2                  15                 18
  T3                  44                 30
  T4                   2                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  20P GAIN MUTATED   32 34  6  4
  20P GAIN WILD-TYPE 32 20  5  2
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               32                 32
  N1               34                 20
  N2                6                  5
  N3                4                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  20P GAIN MUTATED   60  1   3 10
  20P GAIN WILD-TYPE 51  1   0  7
D36V6, multiclass
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0                60                 51
  M1                 1                  1
  M1A                3                  0
  MX                10                  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"
D36V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   10 78
  20P GAIN WILD-TYPE 11 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     10   78
  20P GAIN WILD-TYPE   11   51
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               10                 11
  MALE                 78                 51
[1] 2 2
[1] FALSE
D36V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED      18                         1    57
  20P GAIN WILD-TYPE    20                         1    36
D36V9, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                   18                 20
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   57                 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"

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   54 38
  20Q GAIN WILD-TYPE 34 16
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                92                 50 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                38                 16 
$`20Q GAIN MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 
        8.94        16.24         4.21        32.45        33.27         0.85 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
        2.63        20.12         0.26         0.53        17.03        23.41 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A939 TCGA-JY-A93C 
        0.46         0.43       122.10         3.68        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       25.28        18.08         3.16         3.45         0.30         4.31 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
        3.52         3.68         3.35        19.50         4.08        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z 
        7.13         7.43         6.94         2.60         0.36         7.40 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL 
       55.50         2.66        35.97        12.92        16.47        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV 
        5.42        21.37         8.71        13.41        27.12        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V 
       46.09        10.36        10.45         0.10         0.13         0.10 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.13         0.07         0.10         0.20         1.18 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        6.35        53.95         9.30         7.00         8.78         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-A8Q7 
        3.42         4.80         8.15         4.44         8.12        36.72 
TCGA-VR-AA7D TCGA-ZR-A9CJ 
        9.17        18.12 

$`20Q GAIN WILD-TYPE`
TCGA-2H-A9GL TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 
        5.92        20.09        20.78         0.03         0.99         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.36         0.13        14.86        44.75        60.39        68.02 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43M 
       41.52        42.77        25.41        17.59         6.21         8.94 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A891 
        8.78         6.41         3.32         8.71        25.12         3.95 
TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NU TCGA-LN-A49K 
        3.02        13.48        13.55         7.76        83.24         0.07 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y 
        0.16         0.07         0.33         0.07         0.07         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.10         0.10         0.07         0.07         0.10         0.07 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EU 
       17.62         5.16         3.78        14.01         8.48        18.31 
TCGA-VR-AA4G TCGA-VR-AA7I 
       12.03        15.91 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.07               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            122.10              83.24 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              7.61               6.31 
[1] "0.1 - 122.1 (7.6)" "0.0 - 83.2 (6.3)" 
[1] "hr=" "1.2"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED         5        3        3        1        17        16
  20Q GAIN WILD-TYPE       3        1        3        0        18        10
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED          16          8          5          4        2
  20Q GAIN WILD-TYPE         7          3          3          2        1
                    vv
clus                 STAGE IVA
  20Q GAIN MUTATED           2
  20Q GAIN WILD-TYPE         0
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   5                  3
  STAGE IA                  3                  1
  STAGE IB                  3                  3
  STAGE II                  1                  0
  STAGE IIA                17                 18
  STAGE IIB                16                 10
  STAGE III                16                  7
  STAGE IIIA                8                  3
  STAGE IIIB                5                  3
  STAGE IIIC                4                  2
  STAGE IV                  2                  1
  STAGE IVA                 2                  0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  20Q GAIN MUTATED      21 15 47  1
  20Q GAIN WILD-TYPE     5 18 27  3
D37V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1               21                  5
  T2                  15                 18
  T3                  47                 27
  T4                   1                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  20Q GAIN MUTATED   34 39  6  4
  20Q GAIN WILD-TYPE 30 15  5  2
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               34                 30
  N1               39                 15
  N2                6                  5
  N3                4                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  20Q GAIN MUTATED   65  1   3 11
  20Q GAIN WILD-TYPE 46  1   0  6
D37V6, multiclass
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0                65                 46
  M1                 1                  1
  M1A                3                  0
  MX                11                  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"
D37V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   11 86
  20Q GAIN WILD-TYPE 10 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     11   86
  20Q GAIN WILD-TYPE   10   43
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               11                 10
  MALE                 86                 43
[1] 2 2
[1] FALSE
D37V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED      19                         1    63
  20Q GAIN WILD-TYPE    19                         1    30
D37V9, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                   19                 19
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   63                 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"

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED   11  2
  21Q GAIN WILD-TYPE 77 52
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                13                129 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 52 
$`21Q GAIN MUTATED`
TCGA-IG-A3YB TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A93E TCGA-L5-A4OF 
        2.63        23.41         0.46         0.43        18.08         3.68 
TCGA-L5-A8NE TCGA-L5-A8NN TCGA-LN-A49L TCGA-LN-A49U TCGA-LN-A49V TCGA-S8-A6BV 
       55.50         5.42        10.45         0.07         0.10         8.78 
TCGA-V5-A7RC 
        3.42 

$`21Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       20.09         0.85        20.78        20.12         0.03         0.26 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        0.99         0.53        17.03         0.79         0.36         0.13 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       14.86       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        15.48        23.18        25.28 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       17.59         6.21         3.16         3.45         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        8.94         3.52         3.35        19.50         8.78         6.41 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
        4.08        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       30.74         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        8.71         2.60        25.12         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         7.76        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       27.12        83.24        52.57        46.09        10.36         0.07 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W 
        0.16         0.07         0.33         0.10         0.13         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10         0.07         0.13         0.07         0.10         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10         0.07         0.07         0.10         0.07         0.20 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        1.18        17.62         5.16         3.78         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
        9.30         7.00        14.01         5.29         4.80         8.48 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.15         4.44        18.31         8.12        36.72        12.03 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        9.17        15.91        18.12 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.07               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              55.5              122.1 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              3.68               7.63 
[1] "0.1 - 55.5 (3.7)"  "0.0 - 122.1 (7.6)"
[1] "hr=" "2"  
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q GAIN MUTATED         0        0        0        0         5         3
  21Q GAIN WILD-TYPE       8        4        6        1        30        23
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           1          3          1          0        0
  21Q GAIN WILD-TYPE        22          8          7          6        3
                    vv
clus                 STAGE IVA
  21Q GAIN MUTATED           0
  21Q GAIN WILD-TYPE         2
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  0                  4
  STAGE IB                  0                  6
  STAGE II                  0                  1
  STAGE IIA                 5                 30
  STAGE IIB                 3                 23
  STAGE III                 1                 22
  STAGE IIIA                3                  8
  STAGE IIIB                1                  7
  STAGE IIIC                0                  6
  STAGE IV                  0                  3
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  21Q GAIN MUTATED       1  2 10  0
  21Q GAIN WILD-TYPE    25 31 64  4
D38V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1                1                 25
  T2                   2                 31
  T3                  10                 64
  T4                   0                  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                 N0 N1 N2 N3
  21Q GAIN MUTATED    5  6  1  0
  21Q GAIN WILD-TYPE 59 48 10  6
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                5                 59
  N1                6                 48
  N2                1                 10
  N3                0                  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                  M0  M1 M1A  MX
  21Q GAIN MUTATED    11   0   0   1
  21Q GAIN WILD-TYPE 100   2   3  16
D38V6, multiclass
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                11                100
  M1                 0                  2
  M1A                0                  3
  MX                 1                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     1  13
  21Q GAIN WILD-TYPE  20 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   13
  21Q GAIN WILD-TYPE   20  116
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                1                 20
  MALE                 13                116
[1] 2 2
[1] FALSE
D38V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       6                         1     7
  21Q GAIN WILD-TYPE    32                         1    86
D38V9, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    6                 32
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                    7                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   14  5
  22Q GAIN WILD-TYPE 74 49
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                19                123 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 49 
$`22Q GAIN MUTATED`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A97H TCGA-L5-A43E TCGA-L5-A43J 
       20.09         0.85        20.78         0.43         3.45         4.31 
TCGA-L5-A4OM TCGA-L5-A8NT TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 
        4.08        27.12         0.13         0.10         0.10         0.07 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC 
        0.10         0.07         0.20         5.16        14.01         3.42 
TCGA-VR-A8EW 
        8.12 

$`22Q GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12         0.03         0.26         0.99         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41         0.36         0.13        14.86 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        0.46       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        15.48        23.18        25.28 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M 
       18.08        17.59         6.21         3.16         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.52         3.68         3.35        19.50         8.78         6.41 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        30.74 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        4.90        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        2.60        25.12         0.36         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
       55.50         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.42        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        83.24        52.57        46.09        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45         0.16         0.07         0.33         0.10         0.13 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 
        0.07         0.10         0.07         0.10         0.07         0.07 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.10         0.07         1.18        17.62         3.78         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
       53.95         9.30         7.00         8.78         5.29         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.48         8.15         4.44        18.31        36.72        12.03 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        9.17        15.91        18.12 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.07               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             27.12             122.10 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              3.42               8.15 
[1] "0.1 - 27.1 (3.4)"  "0.0 - 122.1 (8.2)"
[1] "hr=" "1.4"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         1        1        1        1         8         4
  22Q GAIN WILD-TYPE       7        3        5        0        27        22
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           2          2          2          0        0
  22Q GAIN WILD-TYPE        21          9          6          6        3
                    vv
clus                 STAGE IVA
  22Q GAIN MUTATED           0
  22Q GAIN WILD-TYPE         2
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  1                  3
  STAGE IB                  1                  5
  STAGE II                  1                  0
  STAGE IIA                 8                 27
  STAGE IIB                 4                 22
  STAGE III                 2                 21
  STAGE IIIA                2                  9
  STAGE IIIB                2                  6
  STAGE IIIC                0                  6
  STAGE IV                  0                  3
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  22Q GAIN MUTATED       2  7 11  2
  22Q GAIN WILD-TYPE    24 26 63  2
D39V4, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1                2                 24
  T2                   7                 26
  T3                  11                 63
  T4                   2                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  22Q GAIN MUTATED   16  3  2  0
  22Q GAIN WILD-TYPE 48 51  9  6
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               16                 48
  N1                3                 51
  N2                2                  9
  N3                0                  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                 M0 M1 M1A MX
  22Q GAIN MUTATED   19  0   0  2
  22Q GAIN WILD-TYPE 92  2   3 15
D39V6, multiclass
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0                19                 92
  M1                 0                  2
  M1A                0                  3
  MX                 2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     2  21
  22Q GAIN WILD-TYPE  19 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2   21
  22Q GAIN WILD-TYPE   19  108
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                2                 19
  MALE                 21                108
[1] 2 2
[1] FALSE
D39V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED      13                         1     9
  22Q GAIN WILD-TYPE    25                         1    84
D39V9, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                   13                 25
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                    9                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED   17  9
  XQ GAIN WILD-TYPE 71 45
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               26               116 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                9                45 
$`XQ GAIN MUTATED`
TCGA-2H-A9GI TCGA-IG-A3QL TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       14.30        20.09         0.26         0.53        17.03        23.41 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OQ 
        0.13         0.46       122.10         4.31         8.78         1.38 
TCGA-L5-A88Y TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49V 
        0.36         5.42        21.37         0.07         0.13         0.10 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-S8-A6BV TCGA-V5-AASV TCGA-VR-A8EU 
        0.10         0.13         0.10         8.78         8.48        18.31 
TCGA-VR-A8EW TCGA-ZR-A9CJ 
        8.12        18.12 

$`XQ GAIN WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 
        8.94        16.24         4.21        32.45        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 
       20.78         2.63        20.12         0.03         0.99         0.79 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.36        14.86         0.43        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.68        41.52        42.77        25.41        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       25.28        18.08        17.59         6.21         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         8.94         3.52         3.68         3.35        19.50 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR 
        6.41         4.08        18.35         3.32         7.17         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       30.74         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
       55.50         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       13.55        13.22         7.76         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       83.24        52.57        46.09        10.36        10.45         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y 
        0.07         0.33         0.10         0.07         0.07         0.07 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.07         0.10         0.10         0.07         0.07         0.10 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.07         0.20         1.18        17.62         5.16         3.78 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        6.35        53.95         9.30         7.00        14.01         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8Q7 TCGA-VR-AA4G 
        3.42         4.80         8.15         4.44        36.72        12.03 
TCGA-VR-AA7D TCGA-VR-AA7I 
        9.17        15.91 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.07              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           122.10             83.24 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            4.865             7.610 
[1] "0.1 - 122.1 (4.9)" "0.0 - 83.2 (7.6)" 
[1] "hr=" "1.1"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         1        0        0        0         8         6
  XQ GAIN WILD-TYPE       7        4        6        1        27        20
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED           3          3          3          2        1
  XQ GAIN WILD-TYPE        20          8          5          4        2
                   vv
clus                STAGE IVA
  XQ GAIN MUTATED           0
  XQ GAIN WILD-TYPE         2
D40V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 4
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                8                27
  STAGE IIB                6                20
  STAGE III                3                20
  STAGE IIIA               3                 8
  STAGE IIIB               3                 5
  STAGE IIIC               2                 4
  STAGE IV                 1                 2
  STAGE IVA                0                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  XQ GAIN MUTATED       4  4 20  0
  XQ GAIN WILD-TYPE    22 29 54  4
D40V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1               4                22
  T2                  4                29
  T3                 20                54
  T4                  0                 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                N0 N1 N2 N3
  XQ GAIN MUTATED   14  8  4  2
  XQ GAIN WILD-TYPE 50 46  7  4
D40V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              14                50
  N1               8                46
  N2               4                 7
  N3               2                 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                M0 M1 M1A MX
  XQ GAIN MUTATED   20  1   0  7
  XQ GAIN WILD-TYPE 91  1   3 10
D40V6, multiclass
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0               20                91
  M1                1                 1
  M1A               0                 3
  MX                7                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     1  27
  XQ GAIN WILD-TYPE  20 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   27
  XQ GAIN WILD-TYPE   20  102
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               1                20
  MALE                27               102
[1] 2 2
[1] FALSE
D40V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED      11                         1    15
  XQ GAIN WILD-TYPE    27                         1    78
D40V9, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                  11                27
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  15                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   17 12
  1P LOSS WILD-TYPE 71 42
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               29               113 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               12                42 
$`1P LOSS MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A4P3 
       14.30         7.63        16.24        32.45        33.27         0.03 
TCGA-JY-A6FB TCGA-JY-A93C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        23.18         0.30         8.94         3.52         3.35 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NG 
        4.90        29.00         2.60         7.40        55.50        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.92        16.47         1.18         8.02         7.59         5.06 
TCGA-R6-A6XQ TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        6.35        14.01         4.80         8.15         4.44 

$`1P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        58.55         5.92        13.94         8.94 
TCGA-2H-A9GQ TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        4.21        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        0.26         0.99         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
        0.36         0.13        14.86         0.46         0.43       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       44.75        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       15.48        25.28        18.08        17.59         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.45         4.31         3.68        19.50         8.78         6.41 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
        4.08        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
       30.74         7.13         7.43         6.94         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NK 
        0.36         3.95         3.02         2.66        13.48        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.42        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       27.12        83.24        52.57        46.09        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45         0.16         0.07         0.33         0.10         0.13 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        0.07         0.10         0.07         0.10         0.07         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.07         0.10         0.10         0.10         0.07         0.07 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.10         0.07         0.20        17.62         5.16         3.78 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO 
       14.70         7.04        29.59        53.95         9.30         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-A8EW 
        8.78         5.29         3.42         8.48        18.31         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
       36.72        12.03         9.17        15.91        18.12 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.03              0.07 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            60.39            122.10 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             8.02              7.13 
[1] "0.0 - 60.4 (8.0)"  "0.1 - 122.1 (7.1)"
[1] "hr=" "1"  
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED         2        0        2        0         7         2
  1P LOSS WILD-TYPE       6        4        4        1        28        24
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED           6          0          2          0        2
  1P LOSS WILD-TYPE        17         11          6          6        1
                   vv
clus                STAGE IVA
  1P LOSS MUTATED           1
  1P LOSS WILD-TYPE         1
D41V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 0                 4
  STAGE IB                 2                 4
  STAGE II                 0                 1
  STAGE IIA                7                28
  STAGE IIB                2                24
  STAGE III                6                17
  STAGE IIIA               0                11
  STAGE IIIB               2                 6
  STAGE IIIC               0                 6
  STAGE IV                 2                 1
  STAGE IVA                1                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  1P LOSS MUTATED       5  6 14  0
  1P LOSS WILD-TYPE    21 27 60  4
D41V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1               5                21
  T2                  6                27
  T3                 14                60
  T4                  0                 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                N0 N1 N2 N3
  1P LOSS MUTATED   11 11  3  0
  1P LOSS WILD-TYPE 53 43  8  6
D41V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              11                53
  N1              11                43
  N2               3                 8
  N3               0                 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                M0 M1 M1A MX
  1P LOSS MUTATED   18  1   2  3
  1P LOSS WILD-TYPE 93  1   1 14
D41V6, multiclass
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               18                93
  M1                1                 1
  M1A               2                 1
  MX                3                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     5  26
  1P LOSS WILD-TYPE  16 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      5   26
  1P LOSS WILD-TYPE   16  103
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               5                16
  MALE                26               103
[1] 2 2
[1] FALSE
D41V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       4                         0    22
  1P LOSS WILD-TYPE    34                         2    71
D41V9, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   4                34
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  22                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED    9  8
  1Q LOSS WILD-TYPE 79 46
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               17               125 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                8                46 
$`1Q LOSS MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IG-A3I8 TCGA-IG-A4QS TCGA-L5-A43M TCGA-L5-A4OE 
        7.63        16.24        33.27         0.26         8.94         3.52 
TCGA-L5-A4OT TCGA-L5-A88V TCGA-LN-A49O TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ 
        4.90         2.60         0.33         1.18         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASX 
        5.06         6.35        14.01         4.80         4.44 

$`1Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        8.94         4.21        32.45        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12         0.03         0.99         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41         0.36         0.13        14.86         0.46 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        0.43       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        15.48        23.18        25.28 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       18.08        17.59         6.21         3.16         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        4.31         3.68         3.35        19.50         8.78         6.41 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
        4.08        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
       30.74        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        2.66        35.97        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.42        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       27.12        83.24        52.57        46.09        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.45         0.16         0.07         0.10         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10         0.07         0.10         0.07         0.13         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10         0.10         0.10         0.07         0.07         0.10 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 
        0.07         0.20        17.62         5.16         3.78        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
        7.04        29.59        53.95         9.30         7.00         8.78 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8EW 
        5.29         3.42         8.48         8.15        18.31         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
       36.72        12.03         9.17        15.91        18.12 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.26              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            33.27            122.10 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             5.06              8.12 
[1] "0.3 - 33.3 (5.1)"  "0.0 - 122.1 (8.1)"
[1] "hr=" "2.1"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         0        0        2        0         3         0
  1Q LOSS WILD-TYPE       8        4        4        1        32        26
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED           2          0          2          0        1
  1Q LOSS WILD-TYPE        21         11          6          6        2
                   vv
clus                STAGE IVA
  1Q LOSS MUTATED           1
  1Q LOSS WILD-TYPE         1
D42V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 0                 4
  STAGE IB                 2                 4
  STAGE II                 0                 1
  STAGE IIA                3                32
  STAGE IIB                0                26
  STAGE III                2                21
  STAGE IIIA               0                11
  STAGE IIIB               2                 6
  STAGE IIIC               0                 6
  STAGE IV                 1                 2
  STAGE IVA                1                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  1Q LOSS MUTATED       1  2  9  0
  1Q LOSS WILD-TYPE    25 31 65  4
D42V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1               1                25
  T2                  2                31
  T3                  9                65
  T4                  0                 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                N0 N1 N2 N3
  1Q LOSS MUTATED    5  4  3  0
  1Q LOSS WILD-TYPE 59 50  8  6
D42V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0               5                59
  N1               4                50
  N2               3                 8
  N3               0                 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                 M0  M1 M1A  MX
  1Q LOSS MUTATED     6   0   2   3
  1Q LOSS WILD-TYPE 105   2   1  14
D42V6, multiclass
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0                6               105
  M1                0                 2
  M1A               2                 1
  MX                3                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3  14
  1Q LOSS WILD-TYPE  18 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3   14
  1Q LOSS WILD-TYPE   18  115
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               3                18
  MALE                14               115
[1] 2 2
[1] FALSE
D42V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       2                         0    12
  1Q LOSS WILD-TYPE    36                         2    81
D42V9, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   2                36
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  12                81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED    6  0
  2P LOSS WILD-TYPE 82 54
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                6               136 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                0                54 
$`2P LOSS MUTATED`
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-L5-A4OS TCGA-L5-A8NE TCGA-L5-A8NK TCGA-VR-A8Q7 
        2.63        20.12        30.74        55.50        13.55        36.72 

$`2P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.09         0.85        20.78         0.03         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86         0.46         0.43       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        15.48 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        25.28        18.08        17.59         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.45         0.30         4.31         8.94         3.52         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.35        19.50         8.78         6.41         4.08        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38         3.16         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG 
        0.36         7.40         3.95         3.02         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.22         7.76         5.42 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       21.37         8.71        13.41        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         0.07        10.45         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
        0.33         0.10         0.13         0.07         0.10         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10         0.07         0.13         0.07         0.10         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10         0.07         0.07         0.10         0.07         0.20 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        1.18        17.62         5.16         3.78         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        9.30         7.00         8.78        14.01         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW 
        4.80         8.48         8.15         4.44        18.31         8.12 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
       12.03         9.17        15.91        18.12 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.63              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             55.5             122.1 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           25.430             7.285 
[1] "2.6 - 55.5 (25.4)" "0.0 - 122.1 (7.3)"
[1] "hr="     "7.6e+07"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED         0        0        0        0         3         2
  2P LOSS WILD-TYPE       8        4        6        1        32        24
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED           0          3          0          0        0
  2P LOSS WILD-TYPE        23          8          8          6        3
                   vv
clus                STAGE IVA
  2P LOSS MUTATED           0
  2P LOSS WILD-TYPE         2
D43V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 0                 4
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                3                32
  STAGE IIB                2                24
  STAGE III                0                23
  STAGE IIIA               3                 8
  STAGE IIIB               0                 8
  STAGE IIIC               0                 6
  STAGE IV                 0                 3
  STAGE IVA                0                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  2P LOSS MUTATED       0  4  4  0
  2P LOSS WILD-TYPE    26 29 70  4
D43V4, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1               0                26
  T2                  4                29
  T3                  4                70
  T4                  0                 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                N0 N1 N2 N3
  2P LOSS MUTATED    3  5  0  0
  2P LOSS WILD-TYPE 61 49 11  6
D43V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0               3                61
  N1               5                49
  N2               0                11
  N3               0                 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                 M0  M1 M1A  MX
  2P LOSS MUTATED     8   0   0   0
  2P LOSS WILD-TYPE 103   2   3  17
D43V6, multiclass
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0                8               103
  M1                0                 2
  M1A               0                 3
  MX                0                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     2   6
  2P LOSS WILD-TYPE  19 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    6
  2P LOSS WILD-TYPE   19  123
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               2                19
  MALE                 6               123
[1] 2 2
[1] FALSE
D43V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       2                         0     6
  2P LOSS WILD-TYPE    36                         2    87
D43V9, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   2                36
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                   6                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    9  4
  2Q LOSS WILD-TYPE 79 50
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               13               129 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                4                50 
$`2Q LOSS MUTATED`
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-L5-A43H TCGA-L5-A4OS 
        2.63        20.12         0.03         0.79         0.30        30.74 
TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-LN-A49L TCGA-LN-A49Y TCGA-LN-A4MQ 
        3.02        16.47        13.55        10.45         0.07         0.10 
TCGA-VR-A8Q7 
       36.72 

$`2Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.09         0.85        20.78         0.26         0.99         0.53 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03        23.41         0.36         0.13        14.86         0.46 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        0.43       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        15.48        23.18        25.28 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J 
       18.08        17.59         6.21         3.16         3.45         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        8.94         3.52         3.68         3.35        19.50         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
        6.41         4.08        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        8.71         2.60        25.12         0.36         7.40         3.95 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NL 
       55.50         2.66        35.97        12.92        13.48        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.42        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
       83.24        52.57        46.09        10.36         0.07         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
        0.07         0.33         0.10         0.13         0.07         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.07         0.10         0.13         0.07         0.10         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.07         0.07         0.07         0.20         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       17.62         5.16         3.78         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        7.00         8.78        14.01         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G 
        8.48         8.15         4.44        18.31         8.12        12.03 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        9.17        15.91        18.12 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.03              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            36.72            122.10 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             3.02              7.59 
[1] "0.0 - 36.7 (3.0)"  "0.1 - 122.1 (7.6)"
[1] "hr=" "1"  
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED         1        0        1        0         5         2
  2Q LOSS WILD-TYPE       7        4        5        1        30        24
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED           3          3          0          0        0
  2Q LOSS WILD-TYPE        20          8          8          6        3
                   vv
clus                STAGE IVA
  2Q LOSS MUTATED           0
  2Q LOSS WILD-TYPE         2
D44V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  1                 7
  STAGE IA                 0                 4
  STAGE IB                 1                 5
  STAGE II                 0                 1
  STAGE IIA                5                30
  STAGE IIB                2                24
  STAGE III                3                20
  STAGE IIIA               3                 8
  STAGE IIIB               0                 8
  STAGE IIIC               0                 6
  STAGE IV                 0                 3
  STAGE IVA                0                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  2Q LOSS MUTATED       1  5  9  0
  2Q LOSS WILD-TYPE    25 28 65  4
D44V4, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1               1                25
  T2                  5                28
  T3                  9                65
  T4                  0                 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                N0 N1 N2 N3
  2Q LOSS MUTATED    7  8  0  0
  2Q LOSS WILD-TYPE 57 46 11  6
D44V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0               7                57
  N1               8                46
  N2               0                11
  N3               0                 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                M0 M1 M1A MX
  2Q LOSS MUTATED   15  0   0  0
  2Q LOSS WILD-TYPE 96  2   3 17
D44V6, multiclass
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0               15                96
  M1                0                 2
  M1A               0                 3
  MX                0                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     3  12
  2Q LOSS WILD-TYPE  18 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3   12
  2Q LOSS WILD-TYPE   18  117
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               3                18
  MALE                12               117
[1] 2 2
[1] FALSE
D44V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       5                         0    10
  2Q LOSS WILD-TYPE    33                         2    83
D44V9, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   5                33
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  10                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED   46 21
  3P LOSS WILD-TYPE 42 33
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               67                75 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               21                33 
$`3P LOSS MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       14.30        13.94         4.21        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
       20.78         2.63        20.12         0.26         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FD TCGA-JY-A938 
        0.79        23.41         0.13         0.43        68.02        25.41 
TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO 
        3.45         8.94         3.35        19.50         6.41         3.32 
TCGA-L5-A4OP TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z 
        7.17         7.13         7.43         6.94         2.60         7.40 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NS 
        2.66        35.97        12.92        16.47        13.55        13.41 
TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X 
        0.07         0.07         0.33         0.13         0.07         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.07         0.13         0.07         0.10         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 
        0.07         0.10         0.07         0.20         1.18        17.62 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        7.59         7.04         6.35         7.00         8.78        14.01 
TCGA-V5-A7RC TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
        3.42        18.31         8.12        36.72        12.03         9.17 
TCGA-VR-AA7I 
       15.91 

$`3P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A7DP 
       16.24        32.45         0.03         0.99         0.36        14.86 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG 
        0.46       122.10        44.75        60.39         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       42.77        15.48        23.18        25.28        18.08        17.59 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF 
        6.21         3.16         0.30         4.31         3.52         3.68 
TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        8.78         4.08        18.35         1.38         3.16        30.74 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 
        4.90        29.00         8.71        25.12         0.36         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        3.02        55.50        13.48        13.22         7.76         5.42 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49W 
       10.36        10.45         0.16         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.07         5.16         3.78         8.02         5.06        14.70 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
       29.59        53.95         9.30         5.29         4.80         8.48 
TCGA-V5-AASW TCGA-V5-AASX TCGA-ZR-A9CJ 
        8.15         4.44        18.12 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.07              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            68.02            122.10 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             6.94              8.71 
[1] "0.1 - 68.0 (6.9)"  "0.0 - 122.1 (8.7)"
[1] "hr=" "1.2"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED         4        1        3        1        23        12
  3P LOSS WILD-TYPE       4        3        3        0        12        14
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED          10          8          2          2        2
  3P LOSS WILD-TYPE        13          3          6          4        1
                   vv
clus                STAGE IVA
  3P LOSS MUTATED           1
  3P LOSS WILD-TYPE         1
D45V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  4                 4
  STAGE IA                 1                 3
  STAGE IB                 3                 3
  STAGE II                 1                 0
  STAGE IIA               23                12
  STAGE IIB               12                14
  STAGE III               10                13
  STAGE IIIA               8                 3
  STAGE IIIB               2                 6
  STAGE IIIC               2                 4
  STAGE IV                 2                 1
  STAGE IVA                1                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  3P LOSS MUTATED      12 17 38  3
  3P LOSS WILD-TYPE    14 16 36  1
D45V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1              12                14
  T2                 17                16
  T3                 38                36
  T4                  3                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  3P LOSS MUTATED   39 24  4  2
  3P LOSS WILD-TYPE 25 30  7  4
D45V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              39                25
  N1              24                30
  N2               4                 7
  N3               2                 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                M0 M1 M1A MX
  3P LOSS MUTATED   61  2   1  6
  3P LOSS WILD-TYPE 50  0   2 11
D45V6, multiclass
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0               61                50
  M1                2                 0
  M1A               1                 2
  MX                6                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"
D45V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   13 61
  3P LOSS WILD-TYPE  8 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     13   61
  3P LOSS WILD-TYPE    8   68
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              13                 8
  MALE                61                68
[1] 2 2
[1] FALSE
D45V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED      27                         1    39
  3P LOSS WILD-TYPE    11                         1    54
D45V9, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                  27                11
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  39                54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED   12  9
  3Q LOSS WILD-TYPE 76 45
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               21               121 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9                45 
$`3Q LOSS MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3YA TCGA-IG-A5S3 
       14.30        13.94         4.21        32.45        20.78        23.41 
TCGA-JY-A938 TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OX TCGA-L5-A88Z 
       25.41         3.45        19.50         3.32         7.43         7.40 
TCGA-L5-A8NH TCGA-LN-A49K TCGA-LN-A49U TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A5U6 
       12.92         0.07         0.07         0.07         0.10         0.20 
TCGA-LN-A5U7 TCGA-R6-A6XQ TCGA-RE-A7BO 
        1.18         6.35         7.00 

$`3Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC 
       16.24        33.27        20.09         0.85         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
        0.03         0.26         0.99         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
        0.36         0.13        14.86         0.46         0.43       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       15.48        23.18        25.28        18.08        17.59         6.21 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.16         0.30         4.31         8.94         3.52         3.68 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
        3.35         8.78         6.41         4.08        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        30.74         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 
        6.94         8.71         2.60        25.12         0.36         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        35.97        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.42        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.41        27.12        83.24        52.57        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45         0.16         0.07         0.33         0.10         0.13 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10         0.07         0.10         0.13         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-M9-A5M8 
        0.10         0.07         0.07         0.10         0.07        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        5.16         3.78         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW 
        7.04        29.59        53.95         9.30         8.78        14.01 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42         4.80         8.48         8.15         4.44 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       18.31         8.12        36.72        12.03         9.17        15.91 
TCGA-ZR-A9CJ 
       18.12 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.07              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            32.45            122.10 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             7.00              7.76 
[1] "0.1 - 32.5 (7.0)"  "0.0 - 122.1 (7.8)"
[1] "hr=" "1.5"
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         2        0        0        1         8         6
  3Q LOSS WILD-TYPE       6        4        6        0        27        20
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED           2          1          0          1        1
  3Q LOSS WILD-TYPE        21         10          8          5        2
                   vv
clus                STAGE IVA
  3Q LOSS MUTATED           0
  3Q LOSS WILD-TYPE         2
D46V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 0                 4
  STAGE IB                 0                 6
  STAGE II                 1                 0
  STAGE IIA                8                27
  STAGE IIB                6                20
  STAGE III                2                21
  STAGE IIIA               1                10
  STAGE IIIB               0                 8
  STAGE IIIC               1                 5
  STAGE IV                 1                 2
  STAGE IVA                0                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  3Q LOSS MUTATED       6  5 10  1
  3Q LOSS WILD-TYPE    20 28 64  3
D46V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1               6                20
  T2                  5                28
  T3                 10                64
  T4                  1                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  3Q LOSS MUTATED   14  7  0  1
  3Q LOSS WILD-TYPE 50 47 11  5
D46V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              14                50
  N1               7                47
  N2               0                11
  N3               1                 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                M0 M1 M1A MX
  3Q LOSS MUTATED   21  1   0  0
  3Q LOSS WILD-TYPE 90  1   3 17
D46V6, multiclass
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               21                90
  M1                1                 1
  M1A               0                 3
  MX                0                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     3  20
  3Q LOSS WILD-TYPE  18 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3   20
  3Q LOSS WILD-TYPE   18  109
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               3                18
  MALE                20               109
[1] 2 2
[1] FALSE
D46V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       8                         0    11
  3Q LOSS WILD-TYPE    30                         2    82
D46V9, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   8                30
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  11                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   45 34
  4P LOSS WILD-TYPE 43 20
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               79                63 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               34                20 
$`4P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
       20.78        20.12         0.03         0.26         0.53         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH 
        0.36         0.13         0.46        44.75        60.39        42.77 
TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       23.18        18.08         3.16         8.94         3.52         3.35 
TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88Z 
        6.41         3.16         4.90         7.13         7.43         7.40 
TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        3.95        35.97        12.92        16.47        13.55        13.22 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
        8.71        13.41        27.12        46.09        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W 
       10.45         0.16         0.07         0.10         0.07         0.07 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ 
        0.10         0.13         0.07         0.10         0.07         0.10 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.07         0.20         1.18         8.02         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
        7.04         6.35         7.00        14.01         3.42         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.15         4.44        18.31         8.12        36.72        12.03 
TCGA-VR-AA7I 
       15.91 

$`4P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 
       31.27         7.63         2.63         0.99        17.03        23.41 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.86         0.43       122.10        68.02         3.68        41.52 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       25.41        15.48        25.28        17.59         6.21         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM 
        0.30         4.31         3.68        19.50         8.78         4.08 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
       18.35         3.32         7.17         1.38        30.74        29.00 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A893 
        6.94         8.71         2.60        25.12         0.36         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       55.50         2.66        13.48         7.76         5.42        21.37 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49Y 
       83.24        52.57         0.33         0.13         0.10         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.10         0.10         0.07        17.62         5.16         3.78 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-V5-A7RB 
       14.70        29.59        53.95         9.30         8.78         5.29 
TCGA-V5-AASV TCGA-VR-AA7D TCGA-ZR-A9CJ 
        8.48         9.17        18.12 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.03              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            60.39            122.10 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             7.13              8.48 
[1] "0.0 - 60.4 (7.1)"  "0.1 - 122.1 (8.5)"
[1] "hr=" "1.8"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED         4        1        4        1        19        13
  4P LOSS WILD-TYPE       4        3        2        0        16        13
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED          14          7          6          1        3
  4P LOSS WILD-TYPE         9          4          2          5        0
                   vv
clus                STAGE IVA
  4P LOSS MUTATED           1
  4P LOSS WILD-TYPE         1
D47V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  4                 4
  STAGE IA                 1                 3
  STAGE IB                 4                 2
  STAGE II                 1                 0
  STAGE IIA               19                16
  STAGE IIB               13                13
  STAGE III               14                 9
  STAGE IIIA               7                 4
  STAGE IIIB               6                 2
  STAGE IIIC               1                 5
  STAGE IV                 3                 0
  STAGE IVA                1                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  4P LOSS MUTATED      11 22 40  3
  4P LOSS WILD-TYPE    15 11 34  1
D47V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1              11                15
  T2                 22                11
  T3                 40                34
  T4                  3                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  4P LOSS MUTATED   34 33  8  1
  4P LOSS WILD-TYPE 30 21  3  5
D47V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              34                30
  N1              33                21
  N2               8                 3
  N3               1                 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                M0 M1 M1A MX
  4P LOSS MUTATED   67  2   2  4
  4P LOSS WILD-TYPE 44  0   1 13
D47V6, multiclass
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0               67                44
  M1                2                 0
  M1A               2                 1
  MX                4                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"
D47V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   11 74
  4P LOSS WILD-TYPE 10 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     11   74
  4P LOSS WILD-TYPE   10   55
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              11                10
  MALE                74                55
[1] 2 2
[1] FALSE
D47V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED      27                         1    45
  4P LOSS WILD-TYPE    11                         1    48
D47V9, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                  27                11
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  45                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   37 32
  4Q LOSS WILD-TYPE 51 22
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               69                73 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               32                22 
$`4Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        20.09         0.85 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6FA 
        0.26         0.53         0.79         0.36         0.46        44.75 
TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43J 
       60.39        42.77        23.18        18.08         3.16         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW 
        8.94         3.52         3.35         3.16         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NH 
        7.43         6.94         7.40         3.95        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
       16.47        13.22         8.71        13.41        27.12        83.24 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R 
       46.09        10.36         0.07        10.45         0.16         0.10 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U6 
        0.07         0.07         0.07         0.10         0.10         0.20 
TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
        1.18         8.02         7.59         5.06         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASW 
        6.35         9.30         7.00        14.01         4.80         8.15 
TCGA-V5-AASX TCGA-VR-A8Q7 TCGA-VR-AA7I 
        4.44        36.72        15.91 

$`4Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       31.27         7.63        20.78         2.63        20.12         0.03 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
        0.99        17.03        23.41         0.13        14.86         0.43 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 
      122.10        68.02         3.68        41.52        25.41        15.48 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       25.28        17.59         6.21         3.45         0.30         3.68 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       19.50         8.78         6.41         4.08        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88V 
        7.17         1.38        30.74        29.00         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI 
       25.12         0.36         3.02        55.50         2.66        13.48 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-LN-A49N 
       13.55         7.76         5.42        21.37        52.57         0.07 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        0.33         0.13         0.10         0.10         0.07         0.13 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-M9-A5M8 
        0.10         0.10         0.07         0.07         0.07        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-S8-A6BV TCGA-V5-A7RB 
        5.16         3.78        14.70        53.95         8.78         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D 
        3.42         8.48        18.31         8.12        12.03         9.17 
TCGA-ZR-A9CJ 
       18.12 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.07              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            83.24            122.10 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             7.43              7.63 
[1] "0.1 - 83.2 (7.4)"  "0.0 - 122.1 (7.6)"
[1] "hr=" "1.5"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED         3        1        5        1        14        11
  4Q LOSS WILD-TYPE       5        3        1        0        21        15
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED          14          4          5          1        2
  4Q LOSS WILD-TYPE         9          7          3          5        1
                   vv
clus                STAGE IVA
  4Q LOSS MUTATED           1
  4Q LOSS WILD-TYPE         1
D48V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  3                 5
  STAGE IA                 1                 3
  STAGE IB                 5                 1
  STAGE II                 1                 0
  STAGE IIA               14                21
  STAGE IIB               11                15
  STAGE III               14                 9
  STAGE IIIA               4                 7
  STAGE IIIB               5                 3
  STAGE IIIC               1                 5
  STAGE IV                 2                 1
  STAGE IVA                1                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  4Q LOSS MUTATED       9 16 37  2
  4Q LOSS WILD-TYPE    17 17 37  2
D48V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1               9                17
  T2                 16                17
  T3                 37                37
  T4                  2                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  4Q LOSS MUTATED   29 28  6  1
  4Q LOSS WILD-TYPE 35 26  5  5
D48V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              29                35
  N1              28                26
  N2               6                 5
  N3               1                 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                M0 M1 M1A MX
  4Q LOSS MUTATED   54  1   2  6
  4Q LOSS WILD-TYPE 57  1   1 11
D48V6, multiclass
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0               54                57
  M1                1                 1
  M1A               2                 1
  MX                6                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"
D48V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    8 66
  4Q LOSS WILD-TYPE 13 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8   66
  4Q LOSS WILD-TYPE   13   63
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               8                13
  MALE                66                63
[1] 2 2
[1] FALSE
D48V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED      21                         0    41
  4Q LOSS WILD-TYPE    17                         2    52
D48V9, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                  21                17
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  41                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED   25 11
  5P LOSS WILD-TYPE 63 43
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               36               106 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               11                43 
$`5P LOSS MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A3QL 
       58.55         7.63        13.94         8.94         4.21        20.09 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB 
        0.26         0.53        17.03         0.46       122.10        60.39 
TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4OS 
        3.45         3.52         3.68         3.35         6.41        30.74 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NN TCGA-L5-A8NR 
        2.60         3.95         3.02         2.66         5.42         8.71 
TCGA-L5-A8NT TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49V TCGA-LN-A4A8 TCGA-M9-A5M8 
       27.12         0.07        10.45         0.10         0.07        17.62 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-V5-AASW TCGA-V5-AASX 
       29.59         6.35         9.30         8.78         8.15         4.44 

$`5P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78        31.27        14.30         5.92        16.24        32.45 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27         0.85        20.78         2.63        20.12         0.03 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.99         0.79        23.41         0.36         0.13        14.86 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
        0.43        44.75        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        15.48        23.18        25.28        18.08        17.59 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OH 
        6.21         3.16         0.30         4.31         8.94        19.50 
TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
        8.78         4.08        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NG 
        8.71        25.12         0.36         7.40        55.50        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       21.37        13.41        83.24        52.57        46.09        10.36 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        0.16         0.07         0.33         0.10         0.13         0.07 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.07         0.10         0.07         0.13         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10         0.10         0.07         0.10         0.07         0.20 
TCGA-LN-A5U7 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        1.18         5.16         3.78         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       14.70         7.04        53.95         7.00        14.01         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 
        3.42         4.80         8.48        18.31         8.12        36.72 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
       12.03         9.17        15.91        18.12 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.07              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           122.10             83.24 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            6.380             7.675 
[1] "0.1 - 122.1 (6.4)" "0.0 - 83.2 (7.7)" 
[1] "hr=" "1.3"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P LOSS MUTATED         7        0        0        0         6         6
  5P LOSS WILD-TYPE       1        4        6        1        29        20
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           7          2          3          0        0
  5P LOSS WILD-TYPE        16          9          5          6        3
                   vv
clus                STAGE IVA
  5P LOSS MUTATED           1
  5P LOSS WILD-TYPE         1
D49V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  7                 1
  STAGE IA                 0                 4
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                6                29
  STAGE IIB                6                20
  STAGE III                7                16
  STAGE IIIA               2                 9
  STAGE IIIB               3                 5
  STAGE IIIC               0                 6
  STAGE IV                 0                 3
  STAGE IVA                1                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  5P LOSS MUTATED      11  4 18  0
  5P LOSS WILD-TYPE    15 29 56  4
D49V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1              11                15
  T2                  4                29
  T3                 18                56
  T4                  0                 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                N0 N1 N2 N3
  5P LOSS MUTATED   16 14  3  0
  5P LOSS WILD-TYPE 48 40  8  6
D49V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              16                48
  N1              14                40
  N2               3                 8
  N3               0                 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                M0 M1 M1A MX
  5P LOSS MUTATED   28  0   1  2
  5P LOSS WILD-TYPE 83  2   2 15
D49V6, multiclass
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               28                83
  M1                0                 2
  M1A               1                 2
  MX                2                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    5 33
  5P LOSS WILD-TYPE 16 96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5   33
  5P LOSS WILD-TYPE   16   96
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               5                16
  MALE                33                96
[1] 2 2
[1] FALSE
D49V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       8                         0    23
  5P LOSS WILD-TYPE    30                         2    70
D49V9, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   8                30
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  23                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED   43 21
  5Q LOSS WILD-TYPE 45 33
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               64                78 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               21                33 
$`5Q LOSS MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       32.45        20.09         2.63        20.12         0.03         0.26 
TCGA-IG-A50L TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH 
        0.53         0.46         0.43       122.10        60.39        42.77 
TCGA-JY-A93D TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ 
       25.28         3.45         3.52         3.68         3.35         6.41 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW 
        4.08         7.17         3.16        30.74         4.90         7.13 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60         0.36         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       35.97        12.92        13.55         5.42         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49U 
       27.12        52.57         0.07        10.45         0.07         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-M9-A5M8 
        0.13         0.10         0.07         0.10         0.20        17.62 
TCGA-Q9-A6FU TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW 
        5.16        29.59         6.35         9.30         8.78        14.01 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-A8Q7 
        8.15         4.44         8.12        36.72 

$`5Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A3I8 TCGA-IG-A3Y9 
       25.78        31.27        14.30         5.92        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
       20.78         0.99        17.03         0.79        23.41         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        0.13        14.86        44.75        68.02         3.68        41.52 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       25.41        15.48        23.18        18.08        17.59         6.21 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI 
        3.16         0.30         4.31         8.94        19.50         8.78 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
       18.35         3.32         1.38        29.00         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
        8.71        25.12         7.40        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49M 
        7.76        21.37        83.24        46.09        10.36         0.16 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.33         0.10         0.13         0.10         0.07         0.10 
TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR 
        0.07         0.07         0.10         0.10         0.07         0.07 
TCGA-LN-A5U7 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        1.18         3.78         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        7.04        53.95         7.00         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        8.48        18.31        12.03         9.17        15.91        18.12 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.03              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           122.10             83.24 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             6.77              7.89 
[1] "0.0 - 122.1 (6.8)" "0.1 - 83.2 (7.9)" 
[1] "hr=" "1.3"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED         7        3        1        0        13        12
  5Q LOSS WILD-TYPE       1        1        5        1        22        14
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED           9          5          5          1        2
  5Q LOSS WILD-TYPE        14          6          3          5        1
                   vv
clus                STAGE IVA
  5Q LOSS MUTATED           2
  5Q LOSS WILD-TYPE         0
D50V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  7                 1
  STAGE IA                 3                 1
  STAGE IB                 1                 5
  STAGE II                 0                 1
  STAGE IIA               13                22
  STAGE IIB               12                14
  STAGE III                9                14
  STAGE IIIA               5                 6
  STAGE IIIB               5                 3
  STAGE IIIC               1                 5
  STAGE IV                 2                 1
  STAGE IVA                2                 0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  5Q LOSS MUTATED      15 14 33  0
  5Q LOSS WILD-TYPE    11 19 41  4
D50V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1              15                11
  T2                 14                19
  T3                 33                41
  T4                  0                 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                N0 N1 N2 N3
  5Q LOSS MUTATED   29 26  5  1
  5Q LOSS WILD-TYPE 35 28  6  5
D50V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              29                35
  N1              26                28
  N2               5                 6
  N3               1                 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                M0 M1 M1A MX
  5Q LOSS MUTATED   49  1   3  6
  5Q LOSS WILD-TYPE 62  1   0 11
D50V6, multiclass
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               49                62
  M1                1                 1
  M1A               3                 0
  MX                6                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"
D50V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   10 57
  5Q LOSS WILD-TYPE 11 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     10   57
  5Q LOSS WILD-TYPE   11   72
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              10                11
  MALE                57                72
[1] 2 2
[1] FALSE
D50V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED      16                         0    41
  5Q LOSS WILD-TYPE    22                         2    52
D50V9, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                  16                22
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  41                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   20  7
  6P LOSS WILD-TYPE 68 47
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               27               115 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                7                47 
$`6P LOSS MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A5S3 TCGA-JY-A6FB TCGA-JY-A93C 
       33.27        20.09         0.53        23.41        60.39        23.18 
TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OR TCGA-L5-A88Y 
        3.16         4.31         8.94         3.35         3.16         0.36 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49N 
       16.47        13.55        83.24        52.57         0.07         0.07 
TCGA-LN-A49O TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A5U7 TCGA-S8-A6BV TCGA-V5-A7RC 
        0.33         0.07         0.13         1.18         8.78         3.42 
TCGA-V5-AASW TCGA-VR-A8EW TCGA-ZR-A9CJ 
        8.15         8.12        18.12 

$`6P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3Y9 
       13.94         8.94        16.24         4.21        32.45         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12         0.03         0.26         0.99 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79         0.36         0.13        14.86         0.46 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        0.43       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       42.77        25.41        15.48        25.28        18.08        17.59 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH 
        6.21         3.45         0.30         3.52         3.68        19.50 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
        8.78         6.41         4.08        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38        30.74         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        6.94         8.71         2.60        25.12         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.02        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.42        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R 
       27.12        46.09        10.36        10.45         0.16         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 
        0.13         0.07         0.10         0.10         0.07         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10         0.10         0.10         0.07         0.07         0.10 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.07         0.20        17.62         5.16         3.78         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
       53.95         9.30         7.00        14.01         5.29         4.80 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
        8.48         4.44        18.31        36.72        12.03         9.17 
TCGA-VR-AA7I 
       15.91 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.07              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            83.24            122.10 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             8.12              7.43 
[1] "0.1 - 83.2 (8.1)"  "0.0 - 122.1 (7.4)"
[1] "hr=" "1.8"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED         2        1        0        0        10         4
  6P LOSS WILD-TYPE       6        3        6        1        25        22
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED           2          2          2          1        0
  6P LOSS WILD-TYPE        21          9          6          5        3
                   vv
clus                STAGE IVA
  6P LOSS MUTATED           0
  6P LOSS WILD-TYPE         2
D51V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 1                 3
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA               10                25
  STAGE IIB                4                22
  STAGE III                2                21
  STAGE IIIA               2                 9
  STAGE IIIB               2                 6
  STAGE IIIC               1                 5
  STAGE IV                 0                 3
  STAGE IVA                0                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  6P LOSS MUTATED       4  4 18  0
  6P LOSS WILD-TYPE    22 29 56  4
D51V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1               4                22
  T2                  4                29
  T3                 18                56
  T4                  0                 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                N0 N1 N2 N3
  6P LOSS MUTATED   17  5  3  1
  6P LOSS WILD-TYPE 47 49  8  5
D51V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              17                47
  N1               5                49
  N2               3                 8
  N3               1                 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                M0 M1 M1A MX
  6P LOSS MUTATED   20  0   0  6
  6P LOSS WILD-TYPE 91  2   3 11
D51V6, multiclass
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               20                91
  M1                0                 2
  M1A               0                 3
  MX                6                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"
D51V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     5  24
  6P LOSS WILD-TYPE  16 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   24
  6P LOSS WILD-TYPE   16  105
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               5                16
  MALE                24               105
[1] 2 2
[1] FALSE
D51V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED      11                         1    16
  6P LOSS WILD-TYPE    27                         1    77
D51V9, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                  11                27
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  16                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   22  7
  6Q LOSS WILD-TYPE 66 47
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               29               113 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7                47 
$`6Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A8O2 TCGA-JY-A6FH TCGA-JY-A93E 
       25.78        33.27        20.09         0.46        42.77        18.08 
TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OR TCGA-L5-A88Y TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.16         8.94         3.16         0.36        16.47        13.55 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49W 
       13.41        83.24        52.57         0.07         0.33         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-R6-A6XG TCGA-S8-A6BV 
        0.13         0.10         0.07         1.18        29.59         8.78 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EW TCGA-ZR-A9CJ 
       14.01         3.42         8.15         8.12        18.12 

$`6Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3Y9 TCGA-IG-A3YA 
        8.94        16.24         4.21        32.45         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12         0.03         0.26         0.99         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41         0.36         0.13        14.86 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        0.43       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       41.52        25.41        15.48        23.18        25.28        17.59 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF 
        6.21         3.45         0.30         4.31         3.52         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.35        19.50         8.78         6.41         4.08        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        7.40         3.95         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       12.92        13.48        13.22         7.76         5.42        21.37 
TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
        8.71        27.12        46.09        10.36        10.45         0.16 
TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
        0.07         0.10         0.13         0.07         0.10         0.10 
TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.07         0.07         0.10         0.10         0.07         0.07 
TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.10         0.20        17.62         5.16         3.78         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59         5.06        14.70         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        9.30         7.00         5.29         4.80         8.48         4.44 
TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       18.31        36.72        12.03         9.17        15.91 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.07              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            83.24            122.10 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             8.78              7.17 
[1] "0.1 - 83.2 (8.8)"  "0.0 - 122.1 (7.2)"
[1] "hr=" "1.9"
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED         0        1        1        0        11         3
  6Q LOSS WILD-TYPE       8        3        5        1        24        23
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           3          2          2          1        0
  6Q LOSS WILD-TYPE        20          9          6          5        3
                   vv
clus                STAGE IVA
  6Q LOSS MUTATED           0
  6Q LOSS WILD-TYPE         2
D52V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 1                 3
  STAGE IB                 1                 5
  STAGE II                 0                 1
  STAGE IIA               11                24
  STAGE IIB                3                23
  STAGE III                3                20
  STAGE IIIA               2                 9
  STAGE IIIB               2                 6
  STAGE IIIC               1                 5
  STAGE IV                 0                 3
  STAGE IVA                0                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  6Q LOSS MUTATED       2  6 18  0
  6Q LOSS WILD-TYPE    24 27 56  4
D52V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1               2                24
  T2                  6                27
  T3                 18                56
  T4                  0                 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                N0 N1 N2 N3
  6Q LOSS MUTATED   16  6  3  1
  6Q LOSS WILD-TYPE 48 48  8  5
D52V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              16                48
  N1               6                48
  N2               3                 8
  N3               1                 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                M0 M1 M1A MX
  6Q LOSS MUTATED   20  0   0  6
  6Q LOSS WILD-TYPE 91  2   3 11
D52V6, multiclass
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0               20                91
  M1                0                 2
  M1A               0                 3
  MX                6                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     3  27
  6Q LOSS WILD-TYPE  18 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3   27
  6Q LOSS WILD-TYPE   18  102
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               3                18
  MALE                27               102
[1] 2 2
[1] FALSE
D52V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED      10                         1    17
  6Q LOSS WILD-TYPE    28                         1    76
D52V9, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                  10                28
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  17                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED    6  5
  7P LOSS WILD-TYPE 82 49
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               11               131 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                5                49 
$`7P LOSS MUTATED`
TCGA-2H-A9GI TCGA-IG-A3Y9 TCGA-JY-A6FD TCGA-L5-A4OM TCGA-L5-A4OU TCGA-L5-A8NE 
       14.30         0.85        68.02         4.08        29.00        55.50 
TCGA-L5-A8NI TCGA-L5-A8NS TCGA-LN-A49L TCGA-LN-A4A8 TCGA-Q9-A6FU 
       13.48        13.41        10.45         0.07         5.16 

$`7P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        20.09 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12         0.03         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86         0.46         0.43       122.10        44.75        60.39 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.68        41.52        42.77        25.41        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       25.28        18.08        17.59         6.21         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        0.30         4.31         8.94         3.52         3.68         3.35 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       19.50         8.78         6.41        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16        30.74         4.90         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        6.94         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ 
        3.95         3.02         2.66        35.97        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.42        21.37         8.71 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       27.12        83.24        52.57        46.09        10.36         0.07 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        0.16         0.07         0.33         0.10         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10         0.07         0.10         0.07         0.13         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.10         0.10         0.10         0.07         0.10         0.07 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.20         1.18        17.62         3.78         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        9.30         7.00         8.78        14.01         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW 
        4.80         8.48         8.15         4.44        18.31         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
       36.72        12.03         9.17        15.91        18.12 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.07              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            68.02            122.10 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            13.41              7.40 
[1] "0.1 - 68.0 (13.4)" "0.0 - 122.1 (7.4)"
[1] "hr=" "1.1"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P LOSS MUTATED         0        1        0        0         4         2
  7P LOSS WILD-TYPE       8        3        6        1        31        24
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED           3          1          1          0        0
  7P LOSS WILD-TYPE        20         10          7          6        3
                   vv
clus                STAGE IVA
  7P LOSS MUTATED           0
  7P LOSS WILD-TYPE         2
D53V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 1                 3
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                4                31
  STAGE IIB                2                24
  STAGE III                3                20
  STAGE IIIA               1                10
  STAGE IIIB               1                 7
  STAGE IIIC               0                 6
  STAGE IV                 0                 3
  STAGE IVA                0                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  7P LOSS MUTATED       1  3  7  1
  7P LOSS WILD-TYPE    25 30 67  3
D53V4, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1               1                25
  T2                  3                30
  T3                  7                67
  T4                  1                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  7P LOSS MUTATED    7  4  1  0
  7P LOSS WILD-TYPE 57 50 10  6
D53V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               7                57
  N1               4                50
  N2               1                10
  N3               0                 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                 M0  M1 M1A  MX
  7P LOSS MUTATED    11   0   0   0
  7P LOSS WILD-TYPE 100   2   3  17
D53V6, multiclass
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               11               100
  M1                0                 2
  M1A               0                 3
  MX                0                17
[1] 4 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
  7P LOSS MUTATED     3   9
  7P LOSS WILD-TYPE  18 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3    9
  7P LOSS WILD-TYPE   18  120
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               3                18
  MALE                 9               120
[1] 2 2
[1] FALSE
D53V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       4                         0     7
  7P LOSS WILD-TYPE    34                         2    86
D53V9, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   4                34
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                   7                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED    9  9
  7Q LOSS WILD-TYPE 79 45
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               18               124 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                9                45 
$`7Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A3Y9 TCGA-IG-A5B8 TCGA-JY-A6FD 
       25.78        14.30         5.92         0.85         0.79        68.02 
TCGA-L5-A4OU TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NR TCGA-L5-A8NS 
       29.00        55.50        13.48        13.55         8.71        13.41 
TCGA-LN-A49L TCGA-LN-A49X TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-V5-AASX TCGA-VR-AA7I 
       10.45         0.10        17.62         5.06         4.44        15.91 

$`7Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB 
        4.21        32.45        33.27        20.09        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12         0.03         0.26         0.99         0.53        17.03 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41         0.36         0.13        14.86         0.46         0.43 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        60.39         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        15.48        23.18        25.28        18.08        17.59 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
        6.21         3.16         3.45         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.52         3.68         3.35        19.50         8.78         6.41 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
        4.08        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
       30.74         4.90         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        2.60        25.12         0.36         7.40         3.95         3.02 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        35.97        12.92        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.42        21.37        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       10.36         0.07         0.16         0.07         0.33         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 
        0.13         0.07         0.10         0.07         0.07         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.07         0.10         0.10         0.10         0.07         0.07 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.10         0.07         0.20         1.18         5.16         3.78 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
       53.95         9.30         7.00         8.78        14.01         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8EW 
        3.42         4.80         8.48         8.15        18.31         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-ZR-A9CJ 
       36.72        12.03         9.17        18.12 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.10              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            68.02            122.10 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           13.445             7.150 
[1] "0.1 - 68.0 (13.4)" "0.0 - 122.1 (7.2)"
[1] "hr=" "1.1"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q LOSS MUTATED         0        0        1        0         6         2
  7Q LOSS WILD-TYPE       8        4        5        1        29        24
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED           7          1          0          0        0
  7Q LOSS WILD-TYPE        16         10          8          6        3
                   vv
clus                STAGE IVA
  7Q LOSS MUTATED           0
  7Q LOSS WILD-TYPE         2
D54V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 0                 4
  STAGE IB                 1                 5
  STAGE II                 0                 1
  STAGE IIA                6                29
  STAGE IIB                2                24
  STAGE III                7                16
  STAGE IIIA               1                10
  STAGE IIIB               0                 8
  STAGE IIIC               0                 6
  STAGE IV                 0                 3
  STAGE IVA                0                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  7Q LOSS MUTATED       0  2 13  2
  7Q LOSS WILD-TYPE    26 31 61  2
D54V4, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1               0                26
  T2                  2                31
  T3                 13                61
  T4                  2                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  7Q LOSS MUTATED   10  7  0  0
  7Q LOSS WILD-TYPE 54 47 11  6
D54V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              10                54
  N1               7                47
  N2               0                11
  N3               0                 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                M0 M1 M1A MX
  7Q LOSS MUTATED   17  0   0  0
  7Q LOSS WILD-TYPE 94  2   3 17
D54V6, multiclass
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0               17                94
  M1                0                 2
  M1A               0                 3
  MX                0                17
[1] 4 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
  7Q LOSS MUTATED     3  16
  7Q LOSS WILD-TYPE  18 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3   16
  7Q LOSS WILD-TYPE   18  113
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               3                18
  MALE                16               113
[1] 2 2
[1] FALSE
D54V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       4                         0    10
  7Q LOSS WILD-TYPE    34                         2    83
D54V9, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   4                34
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  10                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   33 17
  8P LOSS WILD-TYPE 55 37
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               50                92 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               17                37 
$`8P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC 
       25.78         5.92        13.94         0.85         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H 
        0.26         0.53         0.79        23.41         0.13         0.43 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43M 
       44.75        60.39        25.41        23.18        18.08         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OX 
        3.52         3.68        19.50         6.41         3.32         7.43 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NN TCGA-L5-A8NR 
        7.40         3.95        55.50         2.66         5.42         8.71 
TCGA-L5-A8NT TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 
       27.12         0.16         0.07         0.07         0.13         0.10 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.10         0.07         0.20         5.16         3.78         8.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G 
       14.01         5.29         3.42        18.31        36.72        12.03 
TCGA-VR-AA7D TCGA-VR-AA7I 
        9.17        15.91 

$`8P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        14.30        58.55         7.63         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 
        4.21        32.45        33.27        20.09        20.78         0.03 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 
        0.99        17.03         0.36        14.86         0.46       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D 
       68.02         3.68        41.52        42.77        15.48        25.28 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       17.59         6.21         3.16         3.45         0.30         4.31 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
        3.35         8.78         4.08        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        3.16        30.74         4.90        29.00         7.13         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NG 
        8.71         2.60        25.12         0.36         3.02        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       21.37        13.41        83.24        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        0.07        10.45         0.33         0.10         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
        0.10         0.07         0.10         0.07         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.07         0.07         1.18        17.62         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        7.00         8.78         4.80         8.48         8.15         4.44 
TCGA-VR-A8EW TCGA-ZR-A9CJ 
        8.12        18.12 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.07              0.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            60.39            122.10 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            5.670             8.135 
[1] "0.1 - 60.4 (5.7)"  "0.0 - 122.1 (8.1)"
[1] "hr=" "1.1"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED         3        0        2        0         9        11
  8P LOSS WILD-TYPE       5        4        4        1        26        15
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED           6          7          5          2        1
  8P LOSS WILD-TYPE        17          4          3          4        2
                   vv
clus                STAGE IVA
  8P LOSS MUTATED           1
  8P LOSS WILD-TYPE         1
D55V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  3                 5
  STAGE IA                 0                 4
  STAGE IB                 2                 4
  STAGE II                 0                 1
  STAGE IIA                9                26
  STAGE IIB               11                15
  STAGE III                6                17
  STAGE IIIA               7                 4
  STAGE IIIB               5                 3
  STAGE IIIC               2                 4
  STAGE IV                 1                 2
  STAGE IVA                1                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  8P LOSS MUTATED       9 12 27  2
  8P LOSS WILD-TYPE    17 21 47  2
D55V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1               9                17
  T2                 12                21
  T3                 27                47
  T4                  2                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  8P LOSS MUTATED   18 22  7  2
  8P LOSS WILD-TYPE 46 32  4  4
D55V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              18                46
  N1              22                32
  N2               7                 4
  N3               2                 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                M0 M1 M1A MX
  8P LOSS MUTATED   43  1   1  3
  8P LOSS WILD-TYPE 68  1   2 14
D55V6, multiclass
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0               43                68
  M1                1                 1
  M1A               1                 2
  MX                3                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    7 45
  8P LOSS WILD-TYPE 14 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      7   45
  8P LOSS WILD-TYPE   14   84
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               7                14
  MALE                45                84
[1] 2 2
[1] FALSE
D55V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED      14                         1    30
  8P LOSS WILD-TYPE    24                         1    63
D55V9, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                  14                24
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  30                63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED   14  5
  8Q LOSS WILD-TYPE 74 49
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               19               123 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5                49 
$`8Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-IG-A5S3 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A93E 
       25.78         5.92        23.41        44.75        60.39        18.08 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A891 TCGA-L5-A8NE 
        8.94         3.68        19.50         6.41         3.95        55.50 
TCGA-L5-A8NF TCGA-LN-A49N TCGA-LN-A49Y TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-V5-A7RC 
        2.66         0.07         0.07         0.07         0.20         3.42 
TCGA-VR-A8Q7 
       36.72 

$`8Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12         0.03         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03         0.79         0.36         0.13        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        0.46         0.43       122.10        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       42.77        25.41        15.48        23.18        25.28        17.59 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE 
        6.21         3.16         3.45         0.30         4.31         3.52 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
        3.35         8.78         4.08        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        30.74         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.43         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        7.40         3.02        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.42        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.41        27.12        83.24        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        0.07        10.45         0.16         0.33         0.10         0.13 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.07         0.10         0.07         0.10         0.13         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10         0.10         0.10         0.07         0.07         0.10 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        1.18        17.62         5.16         3.78         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        9.30         7.00         8.78        14.01         5.29         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G 
        8.48         8.15         4.44        18.31         8.12        12.03 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        9.17        15.91        18.12 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.07              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            60.39            122.10 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             6.41              7.59 
[1] "0.1 - 60.4 (6.4)"  "0.0 - 122.1 (7.6)"
[1] "hr=" "1.8"
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         3        0        0        0         3         6
  8Q LOSS WILD-TYPE       5        4        6        1        32        20
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED           2          2          0          0        0
  8Q LOSS WILD-TYPE        21          9          8          6        3
                   vv
clus                STAGE IVA
  8Q LOSS MUTATED           1
  8Q LOSS WILD-TYPE         1
D56V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  3                 5
  STAGE IA                 0                 4
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                3                32
  STAGE IIB                6                20
  STAGE III                2                21
  STAGE IIIA               2                 9
  STAGE IIIB               0                 8
  STAGE IIIC               0                 6
  STAGE IV                 0                 3
  STAGE IVA                1                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  8Q LOSS MUTATED       5  6  8  0
  8Q LOSS WILD-TYPE    21 27 66  4
D56V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1               5                21
  T2                  6                27
  T3                  8                66
  T4                  0                 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                N0 N1 N2 N3
  8Q LOSS MUTATED    8 10  1  0
  8Q LOSS WILD-TYPE 56 44 10  6
D56V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0               8                56
  N1              10                44
  N2               1                10
  N3               0                 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                M0 M1 M1A MX
  8Q LOSS MUTATED   16  0   1  1
  8Q LOSS WILD-TYPE 95  2   2 16
D56V6, multiclass
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               16                95
  M1                0                 2
  M1A               1                 2
  MX                1                16
[1] 4 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
  8Q LOSS MUTATED     3  17
  8Q LOSS WILD-TYPE  18 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3   17
  8Q LOSS WILD-TYPE   18  112
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               3                18
  MALE                17               112
[1] 2 2
[1] FALSE
D56V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       6                         1    10
  8Q LOSS WILD-TYPE    32                         1    83
D56V9, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   6                32
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  10                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   52 24
  9P LOSS WILD-TYPE 36 30
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               76                66 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               24                30 
$`9P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        31.27        14.30         8.94        16.24         4.21 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
       20.78        20.12         0.03         0.26         0.53         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FB TCGA-JY-A938 
       23.41         0.13         0.46         0.43        60.39        25.41 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
       18.08         3.16         8.94         3.68        19.50         4.08 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX 
       18.35         3.32         7.17        30.74         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        6.94         2.60         3.95        55.50         2.66        35.97 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ 
       16.47        13.22         8.71        13.41        83.24        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       10.45         0.16         0.07         0.13         0.07         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.10         0.07         0.13         0.07         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 
        0.07         0.10         0.07         0.20         1.18        17.62 
TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        5.16         5.06        14.70        29.59         6.35         9.30 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        8.78         5.29         3.42         4.80         8.15         4.44 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-ZR-A9CJ 
       18.31         8.12        36.72        18.12 

$`9P LOSS WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A3I8 
       58.55         7.63         5.92        13.94        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 
       20.09         0.85         2.63         0.99        17.03         0.36 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.86       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       42.77        15.48        23.18        25.28        17.59         6.21 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI 
        3.45         0.30         4.31         3.52         3.35         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88T 
        6.41         1.38         3.16         4.90        29.00         8.71 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI 
       25.12         0.36         7.40         3.02        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NV 
       13.55         7.76         5.42        21.37        27.12        52.57 
TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A4A4 
       46.09         0.07         0.33         0.10         0.10         0.10 
TCGA-LN-A4A9 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6Y0 
        0.07         3.78         8.02         7.59         7.04        53.95 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        7.00        14.01         8.48        12.03         9.17        15.91 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.03              0.07 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            83.24            122.10 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            6.645             8.250 
[1] "0.0 - 83.2 (6.6)"  "0.1 - 122.1 (8.2)"
[1] "hr=" "1.1"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P LOSS MUTATED         2        2        3        1        19        14
  9P LOSS WILD-TYPE       6        2        3        0        16        12
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED          13          6          4          3        1
  9P LOSS WILD-TYPE        10          5          4          3        2
                   vv
clus                STAGE IVA
  9P LOSS MUTATED           2
  9P LOSS WILD-TYPE         0
D57V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 2                 2
  STAGE IB                 3                 3
  STAGE II                 1                 0
  STAGE IIA               19                16
  STAGE IIB               14                12
  STAGE III               13                10
  STAGE IIIA               6                 5
  STAGE IIIB               4                 4
  STAGE IIIC               3                 3
  STAGE IV                 1                 2
  STAGE IVA                2                 0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  9P LOSS MUTATED      11 20 41  1
  9P LOSS WILD-TYPE    15 13 33  3
D57V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1              11                15
  T2                 20                13
  T3                 41                33
  T4                  1                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  9P LOSS MUTATED   31 33  5  3
  9P LOSS WILD-TYPE 33 21  6  3
D57V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              31                33
  N1              33                21
  N2               5                 6
  N3               3                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  9P LOSS MUTATED   59  1   2  8
  9P LOSS WILD-TYPE 52  1   1  9
D57V6, multiclass
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0               59                52
  M1                1                 1
  M1A               2                 1
  MX                8                 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"
D57V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    8 74
  9P LOSS WILD-TYPE 13 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      8   74
  9P LOSS WILD-TYPE   13   55
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               8                13
  MALE                74                55
[1] 2 2
[1] FALSE
D57V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED      26                         1    44
  9P LOSS WILD-TYPE    12                         1    49
D57V9, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                  26                12
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  44                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"

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   28 18
  9Q LOSS WILD-TYPE 60 36
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               46                96 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               18                36 
$`9Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GO TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
       25.78        31.27        16.24         0.85        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 
        0.03         0.26         0.79        23.41         0.13         0.46 
TCGA-IG-A97H TCGA-JY-A93E TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OS 
        0.43        18.08         8.94         3.68         4.08        30.74 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        7.13         6.94         2.60        55.50         2.66        35.97 
TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       13.22        13.41        83.24        10.36        10.45         0.16 
TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A5U6 
        0.07         0.13         0.07         0.07         0.10         0.20 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-V5-A7RB TCGA-V5-A7RC 
        5.06        29.59         6.35         9.30         5.29         3.42 
TCGA-V5-A7RE TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-ZR-A9CJ 
        4.80         8.12        36.72        18.12 

$`9Q LOSS WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT 
        4.21        32.45        33.27        20.09         2.63         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA 
        0.53        17.03         0.36        14.86       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       15.48        23.18        25.28        17.59         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH 
        3.45         0.30         4.31         3.52         3.35        19.50 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
        8.78         6.41        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W 
        3.16         4.90        29.00         7.43         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI 
        0.36         7.40         3.95         3.02        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55         7.76         5.42        21.37         8.71 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49R 
       27.12        52.57        46.09         0.07         0.33         0.10 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A4 
        0.07         0.10         0.07         0.10         0.13         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 
        0.10         0.07         0.07         0.10         0.07         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       17.62         5.16         3.78         8.02         7.59        14.70 
TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-AASV 
        7.04        53.95         7.00         8.78        14.01         8.48 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        8.15         4.44        18.31        12.03         9.17        15.91 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.03              0.07 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            83.24            122.10 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            6.645             7.695 
[1] "0.0 - 83.2 (6.6)"  "0.1 - 122.1 (7.7)"
[1] "hr=" "1.2"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED         0        1        3        1        10        11
  9Q LOSS WILD-TYPE       8        3        3        0        25        15
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           6          5          3          2        0
  9Q LOSS WILD-TYPE        17          6          5          4        3
                   vv
clus                STAGE IVA
  9Q LOSS MUTATED           2
  9Q LOSS WILD-TYPE         0
D58V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 1                 3
  STAGE IB                 3                 3
  STAGE II                 1                 0
  STAGE IIA               10                25
  STAGE IIB               11                15
  STAGE III                6                17
  STAGE IIIA               5                 6
  STAGE IIIB               3                 5
  STAGE IIIC               2                 4
  STAGE IV                 0                 3
  STAGE IVA                2                 0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  9Q LOSS MUTATED       6 14 24  2
  9Q LOSS WILD-TYPE    20 19 50  2
D58V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1               6                20
  T2                 14                19
  T3                 24                50
  T4                  2                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  9Q LOSS MUTATED   19 20  4  2
  9Q LOSS WILD-TYPE 45 34  7  4
D58V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              19                45
  N1              20                34
  N2               4                 7
  N3               2                 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                M0 M1 M1A MX
  9Q LOSS MUTATED   36  0   2  6
  9Q LOSS WILD-TYPE 75  2   1 11
D58V6, multiclass
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0               36                75
  M1                0                 2
  M1A               2                 1
  MX                6                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    5 46
  9Q LOSS WILD-TYPE 16 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      5   46
  9Q LOSS WILD-TYPE   16   83
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               5                16
  MALE                46                83
[1] 2 2
[1] FALSE
D58V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED      16                         1    28
  9Q LOSS WILD-TYPE    22                         1    65
D58V9, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                  16                22
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  28                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   21 12
  10P LOSS WILD-TYPE 67 42
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                33                109 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                12                 42 
$`10P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A50L 
       25.78        14.30         5.92        33.27         0.85         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A93C TCGA-L5-A43H TCGA-L5-A43J 
        0.79        23.41         0.43        23.18         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OW 
        8.94         3.52         3.35         3.32         4.90         7.13 
TCGA-L5-A8NK TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49O 
       13.55        13.41        27.12        83.24         0.16         0.33 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-Q9-A6FW TCGA-V5-A7RC 
        0.07         0.10         0.07         1.18         3.78         3.42 
TCGA-V5-A7RE TCGA-VR-A8EW TCGA-VR-AA4G 
        4.80         8.12        12.03 

$`10P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        4.21        32.45        20.09        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
        0.03         0.26         0.99        17.03         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86         0.46       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D 
        3.68        41.52        42.77        25.41        15.48        25.28 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF 
       18.08        17.59         6.21         3.16         3.45         3.68 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
       19.50         8.78         6.41         4.08        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        1.38         3.16        30.74        29.00         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        8.71         2.60        25.12         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.02        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.22         7.76         5.42        21.37         8.71 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
       52.57        46.09        10.36         0.07        10.45         0.07 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10         0.13         0.07         0.10         0.07         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.07         0.13         0.07         0.10         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.07         0.20        17.62         5.16         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV 
        9.30         7.00         8.78        14.01         5.29         8.48 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA7D TCGA-VR-AA7I 
        8.15         4.44        18.31        36.72         9.17        15.91 
TCGA-ZR-A9CJ 
       18.12 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.07               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             83.24             122.10 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              4.31               8.15 
[1] "0.1 - 83.2 (4.3)"  "0.0 - 122.1 (8.2)"
[1] "hr=" "1.3"
D59V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P LOSS MUTATED         1        0        2        0        11         5
  10P LOSS WILD-TYPE       7        4        4        1        24        21
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           5          3          4          1        1
  10P LOSS WILD-TYPE        18          8          4          5        2
                    vv
clus                 STAGE IVA
  10P LOSS MUTATED           0
  10P LOSS WILD-TYPE         2
D59V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  0                  4
  STAGE IB                  2                  4
  STAGE II                  0                  1
  STAGE IIA                11                 24
  STAGE IIB                 5                 21
  STAGE III                 5                 18
  STAGE IIIA                3                  8
  STAGE IIIB                4                  4
  STAGE IIIC                1                  5
  STAGE IV                  1                  2
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  10P LOSS MUTATED       2  9 22  1
  10P LOSS WILD-TYPE    24 24 52  3
D59V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1                2                 24
  T2                   9                 24
  T3                  22                 52
  T4                   1                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  10P LOSS MUTATED   18  8  6  1
  10P LOSS WILD-TYPE 46 46  5  5
D59V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               18                 46
  N1                8                 46
  N2                6                  5
  N3                1                  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                 M0 M1 M1A MX
  10P LOSS MUTATED   30  0   1  2
  10P LOSS WILD-TYPE 81  2   2 15
D59V6, multiclass
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0                30                 81
  M1                 0                  2
  M1A                1                  2
  MX                 2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     7  28
  10P LOSS WILD-TYPE  14 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      7   28
  10P LOSS WILD-TYPE   14  101
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                7                 14
  MALE                 28                101
[1] 2 2
[1] FALSE
D59V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED      12                         1    17
  10P LOSS WILD-TYPE    26                         1    76
D59V9, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                   12                 26
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   17                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   24 10
  10Q LOSS WILD-TYPE 64 44
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                34                108 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                10                 44 
$`10Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB 
       25.78        14.30         5.92        33.27         0.85         2.63 
TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43H 
        0.53        23.41         0.43        23.18         3.16         0.30 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NK 
        3.52         3.35         3.32         4.90         7.13        13.55 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A2 
       27.12        83.24         0.16         0.10         0.07         0.13 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10         0.10         0.07         0.10         0.07         0.20 
TCGA-LN-A5U7 TCGA-Q9-A6FU TCGA-V5-A7RC TCGA-V5-A7RE 
        1.18         5.16         3.42         4.80 

$`10Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
        4.21        32.45        20.09        20.78        20.12         0.03 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        0.26         0.99        17.03         0.79         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86         0.46       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D 
        3.68        41.52        42.77        25.41        15.48        25.28 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M 
       18.08        17.59         6.21         3.45         4.31         8.94 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.68        19.50         8.78         6.41         4.08        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX 
        7.17         1.38         3.16        30.74        29.00         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        6.94         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.22         7.76         5.42        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
        8.71        13.41        52.57        46.09        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       10.45         0.07         0.33         0.13         0.07         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-M9-A5M8 
        0.07         0.10         0.07         0.10         0.07        17.62 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        3.78         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
       29.59         6.35        53.95         9.30         7.00         8.78 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU 
       14.01         5.29         8.48         8.15         4.44        18.31 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        8.12        36.72        12.03         9.17        15.91        18.12 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.07               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             83.24             122.10 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             3.240              8.745 
[1] "0.1 - 83.2 (3.2)"  "0.0 - 122.1 (8.7)"
[1] "hr=" "1.2"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED         1        0        1        1        13         4
  10Q LOSS WILD-TYPE       7        4        5        0        22        22
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           7          3          3          1        1
  10Q LOSS WILD-TYPE        16          8          5          5        2
                    vv
clus                 STAGE IVA
  10Q LOSS MUTATED           0
  10Q LOSS WILD-TYPE         2
D60V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  0                  4
  STAGE IB                  1                  5
  STAGE II                  1                  0
  STAGE IIA                13                 22
  STAGE IIB                 4                 22
  STAGE III                 7                 16
  STAGE IIIA                3                  8
  STAGE IIIB                3                  5
  STAGE IIIC                1                  5
  STAGE IV                  1                  2
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  10Q LOSS MUTATED       2 11 21  1
  10Q LOSS WILD-TYPE    24 22 53  3
D60V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1                2                 24
  T2                  11                 22
  T3                  21                 53
  T4                   1                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  10Q LOSS MUTATED   18 12  3  1
  10Q LOSS WILD-TYPE 46 42  8  5
D60V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               18                 46
  N1               12                 42
  N2                3                  8
  N3                1                  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                 M0 M1 M1A MX
  10Q LOSS MUTATED   33  0   1  0
  10Q LOSS WILD-TYPE 78  2   2 17
D60V6, multiclass
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                33                 78
  M1                 0                  2
  M1A                1                  2
  MX                 0                 17
[1] 4 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
  10Q LOSS MUTATED    6 31
  10Q LOSS WILD-TYPE 15 98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      6   31
  10Q LOSS WILD-TYPE   15   98
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                6                 15
  MALE                 31                 98
[1] 2 2
[1] FALSE
D60V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED      17                         1    15
  10Q LOSS WILD-TYPE    21                         1    78
D60V9, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                   17                 21
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   15                 78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   27 10
  11P LOSS WILD-TYPE 61 44
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                37                105 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                10                 44 
$`11P LOSS MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3Y9 TCGA-IG-A3YB 
       31.27        14.30         5.92         4.21         0.85         2.63 
TCGA-JY-A938 TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OG TCGA-L5-A4OO TCGA-L5-A4OP 
       25.41         3.16         0.30         3.35         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE 
        3.16         6.94         2.60         0.36         3.02        55.50 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       16.47        13.55        13.22        10.36        10.45         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.07         0.33         0.10         0.07         0.13         0.07 
TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-V5-A7RE 
        0.10         0.20         5.06        29.59         6.35         4.80 
TCGA-V5-AASW 
        8.15 

$`11P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       32.45        33.27        20.09        20.78        20.12         0.03 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        0.26         0.99         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
        0.36         0.13        14.86         0.46         0.43       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       15.48        23.18        25.28        18.08        17.59         6.21 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH 
        3.45         4.31         8.94         3.52         3.68        19.50 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS 
        8.78         6.41         4.08        18.35         1.38        30.74 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W 
        4.90        29.00         7.13         7.43         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.95         2.66        35.97        12.92        13.48 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.42        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49U 
       83.24        52.57        46.09         0.07         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10         0.10         0.07         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.07         0.10         0.07         1.18        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 
        3.78         8.02         7.59        14.70         7.04        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        9.30         7.00         8.78        14.01         5.29         3.42 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.48         4.44        18.31         8.12        36.72        12.03 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        9.17        15.91        18.12 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.07               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              55.5              122.1 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              3.35               8.71 
[1] "0.1 - 55.5 (3.4)"  "0.0 - 122.1 (8.7)"
[1] "hr=" "1.2"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P LOSS MUTATED         2        2        2        1         6         5
  11P LOSS WILD-TYPE       6        2        4        0        29        21
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED          11          2          0          2        0
  11P LOSS WILD-TYPE        12          9          8          4        3
                    vv
clus                 STAGE IVA
  11P LOSS MUTATED           0
  11P LOSS WILD-TYPE         2
D61V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  2                  2
  STAGE IB                  2                  4
  STAGE II                  1                  0
  STAGE IIA                 6                 29
  STAGE IIB                 5                 21
  STAGE III                11                 12
  STAGE IIIA                2                  9
  STAGE IIIB                0                  8
  STAGE IIIC                2                  4
  STAGE IV                  0                  3
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  11P LOSS MUTATED       7  6 20  1
  11P LOSS WILD-TYPE    19 27 54  3
D61V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1                7                 19
  T2                   6                 27
  T3                  20                 54
  T4                   1                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  11P LOSS MUTATED   16 16  0  2
  11P LOSS WILD-TYPE 48 38 11  4
D61V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               16                 48
  N1               16                 38
  N2                0                 11
  N3                2                  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                 M0 M1 M1A MX
  11P LOSS MUTATED   28  0   0  6
  11P LOSS WILD-TYPE 83  2   3 11
D61V6, multiclass
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                28                 83
  M1                 0                  2
  M1A                0                  3
  MX                 6                 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"
D61V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    4 35
  11P LOSS WILD-TYPE 17 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4   35
  11P LOSS WILD-TYPE   17   94
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                4                 17
  MALE                 35                 94
[1] 2 2
[1] FALSE
D61V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED      12                         0    23
  11P LOSS WILD-TYPE    26                         2    70
D61V9, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                   12                 26
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   23                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   26 14
  11Q LOSS WILD-TYPE 62 40
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                40                102 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                14                 40 
$`11Q LOSS MUTATED`
TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5S3 TCGA-IG-A6QS 
        5.92         4.21        20.12         0.03        23.41         0.13 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OG TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
        3.16         0.30         3.35         4.08         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        3.16         6.94         2.60         3.02        55.50         2.66 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       13.55        13.22        27.12        10.36        10.45         0.16 
TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
        0.10         0.10         0.07         0.13         0.07         0.10 
TCGA-LN-A4A8 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-S8-A6BV 
        0.07         0.20         1.18         5.06         6.35         8.78 
TCGA-V5-A7RC TCGA-VR-A8EU TCGA-VR-AA7D TCGA-VR-AA7I 
        3.42        18.31         9.17        15.91 

$`11Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94        16.24        32.45        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.78         2.63         0.26         0.99         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
        0.79         0.36        14.86         0.46         0.43       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        15.48        23.18        25.28        18.08        17.59 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        6.21         3.45         4.31         8.94         3.52         3.68 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS 
       19.50         8.78         6.41        18.35         1.38        30.74 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W 
        4.90        29.00         7.13         7.43         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        0.36         7.40         3.95        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47         7.76         5.42        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O 
       83.24        52.57        46.09         0.07         0.07         0.33 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.13         0.07         0.10         0.07         0.10         0.10 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.07         0.10         0.07        17.62         5.16         3.78 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 
        8.02         7.59        14.70         7.04        29.59        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
        9.30         7.00        14.01         5.29         4.80         8.48 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-ZR-A9CJ 
        8.15         4.44         8.12        36.72        12.03        18.12 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.03               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              55.5              122.1 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             3.385              8.710 
[1] "0.0 - 55.5 (3.4)"  "0.1 - 122.1 (8.7)"
[1] "hr=" "1.8"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED         2        3        1        1         9         6
  11Q LOSS WILD-TYPE       6        1        5        0        26        20
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED          10          2          0          3        1
  11Q LOSS WILD-TYPE        13          9          8          3        2
                    vv
clus                 STAGE IVA
  11Q LOSS MUTATED           1
  11Q LOSS WILD-TYPE         1
D62V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  3                  1
  STAGE IB                  1                  5
  STAGE II                  1                  0
  STAGE IIA                 9                 26
  STAGE IIB                 6                 20
  STAGE III                10                 13
  STAGE IIIA                2                  9
  STAGE IIIB                0                  8
  STAGE IIIC                3                  3
  STAGE IV                  1                  2
  STAGE IVA                 1                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  11Q LOSS MUTATED       7 10 21  1
  11Q LOSS WILD-TYPE    19 23 53  3
D62V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1                7                 19
  T2                  10                 23
  T3                  21                 53
  T4                   1                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  11Q LOSS MUTATED   20 16  0  3
  11Q LOSS WILD-TYPE 44 38 11  3
D62V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               20                 44
  N1               16                 38
  N2                0                 11
  N3                3                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  11Q LOSS MUTATED   30  1   1  6
  11Q LOSS WILD-TYPE 81  1   2 11
D62V6, multiclass
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                30                 81
  M1                 1                  1
  M1A                1                  2
  MX                 6                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    6 37
  11Q LOSS WILD-TYPE 15 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      6   37
  11Q LOSS WILD-TYPE   15   92
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                6                 15
  MALE                 37                 92
[1] 2 2
[1] FALSE
D62V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED      13                         1    26
  11Q LOSS WILD-TYPE    25                         1    67
D62V9, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                   13                 25
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   26                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED   17 12
  12P LOSS WILD-TYPE 71 42
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                29                113 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                12                 42 
$`12P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A4QS 
       25.78        31.27        13.94        32.45        33.27         0.26 
TCGA-IG-A5B8 TCGA-IG-A97H TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43E 
        0.79         0.43        42.77        25.41        18.08         3.45 
TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW 
        8.94        19.50         7.17         1.38        30.74         7.13 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NV TCGA-LN-A49M 
        3.95         3.02        55.50        12.92        52.57         0.16 
TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-S8-A6BV TCGA-V5-A7RC TCGA-ZR-A9CJ 
        3.78         5.06         8.78         3.42        18.12 

$`12P LOSS WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30        58.55         7.63         5.92         8.94        16.24 
TCGA-2H-A9GQ TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        4.21        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
        0.03         0.99         0.53        17.03        23.41         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
        0.13        14.86         0.46       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        41.52        15.48        23.18        25.28 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE 
       17.59         6.21         3.16         0.30         4.31         3.52 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.68         3.35         8.78         6.41         4.08        18.35 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        3.32         3.16         4.90        29.00         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NF 
        8.71         2.60        25.12         0.36         7.40         2.66 
TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       35.97        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        5.42        21.37         8.71        13.41        27.12        83.24 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.36         0.07        10.45         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10         0.13         0.07         0.10         0.07         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.07         0.13         0.07         0.10         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.07         0.07         0.10         0.07         0.20         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       17.62         5.16         8.02         7.59        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW 
       29.59         6.35        53.95         9.30         7.00        14.01 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU 
        5.29         4.80         8.48         8.15         4.44        18.31 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        8.12        36.72        12.03         9.17        15.91 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.16               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              55.5              122.1 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              8.94               7.40 
[1] "0.2 - 55.5 (8.9)"  "0.0 - 122.1 (7.4)"
[1] "hr=" "1.1"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED         3        1        1        0         5         7
  12P LOSS WILD-TYPE       5        3        5        1        30        19
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED           2          3          2          1        1
  12P LOSS WILD-TYPE        21          8          6          5        2
                    vv
clus                 STAGE IVA
  12P LOSS MUTATED           0
  12P LOSS WILD-TYPE         2
D63V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  1                  3
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 5                 30
  STAGE IIB                 7                 19
  STAGE III                 2                 21
  STAGE IIIA                3                  8
  STAGE IIIB                2                  6
  STAGE IIIC                1                  5
  STAGE IV                  1                  2
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  12P LOSS MUTATED       7  6 15  0
  12P LOSS WILD-TYPE    19 27 59  4
D63V4, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1                7                 19
  T2                   6                 27
  T3                  15                 59
  T4                   0                  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                 N0 N1 N2 N3
  12P LOSS MUTATED   11 11  4  1
  12P LOSS WILD-TYPE 53 43  7  5
D63V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               11                 53
  N1               11                 43
  N2                4                  7
  N3                1                  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                 M0 M1 M1A MX
  12P LOSS MUTATED   22  1   0  5
  12P LOSS WILD-TYPE 89  1   3 12
D63V6, multiclass
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0                22                 89
  M1                 1                  1
  M1A                0                  3
  MX                 5                 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"
D63V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     6  24
  12P LOSS WILD-TYPE  15 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      6   24
  12P LOSS WILD-TYPE   15  105
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                6                 15
  MALE                 24                105
[1] 2 2
[1] FALSE
D63V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       3                         1    20
  12P LOSS WILD-TYPE    35                         1    73
D63V9, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    3                 35
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   20                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED   16  9
  12Q LOSS WILD-TYPE 72 45
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                25                117 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 9                 45 
$`12Q LOSS MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GM TCGA-IG-A3I8 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 
       31.27        13.94        33.27         0.26         0.79        23.41 
TCGA-IG-A97H TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43M 
        0.43        42.77        25.41        18.08         3.45         8.94 
TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A893 TCGA-L5-A8NE 
       19.50         7.17        30.74         7.13         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-S8-A6BV TCGA-V5-A7RC 
        2.66        12.92         3.78         5.06         8.78         3.42 
TCGA-V5-AASX 
        4.44 

$`12Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        14.30        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       16.24         4.21        32.45        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12         0.03         0.99         0.53        17.03 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA 
        0.36         0.13        14.86         0.46       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       60.39        68.02         3.68        41.52        15.48        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J 
       25.28        17.59         6.21         3.16         0.30         4.31 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.52         3.68         3.35         8.78         6.41         4.08 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         3.32         1.38         3.16         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.43         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.40         3.95        35.97        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.42        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       27.12        83.24        52.57        46.09        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45         0.16         0.07         0.33         0.10         0.13 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        0.07         0.10         0.07         0.10         0.07         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.07         0.10         0.10         0.10         0.07         0.07 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.10         0.07         0.20         1.18        17.62         5.16 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
       53.95         9.30         7.00        14.01         5.29         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.48         8.15        18.31         8.12        36.72        12.03 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        9.17        15.91        18.12 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.26               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              55.5              122.1 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              8.78               7.43 
[1] "0.3 - 55.5 (8.8)"  "0.0 - 122.1 (7.4)"
[1] "hr=" "1.2"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q LOSS MUTATED         3        1        1        0         2         8
  12Q LOSS WILD-TYPE       5        3        5        1        33        18
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED           0          2          2          0        1
  12Q LOSS WILD-TYPE        23          9          6          6        2
                    vv
clus                 STAGE IVA
  12Q LOSS MUTATED           1
  12Q LOSS WILD-TYPE         1
D64V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  1                  3
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 2                 33
  STAGE IIB                 8                 18
  STAGE III                 0                 23
  STAGE IIIA                2                  9
  STAGE IIIB                2                  6
  STAGE IIIC                0                  6
  STAGE IV                  1                  2
  STAGE IVA                 1                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  12Q LOSS MUTATED       8  4 10  0
  12Q LOSS WILD-TYPE    18 29 64  4
D64V4, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1                8                 18
  T2                   4                 29
  T3                  10                 64
  T4                   0                  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                 N0 N1 N2 N3
  12Q LOSS MUTATED   10  8  3  0
  12Q LOSS WILD-TYPE 54 46  8  6
D64V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               10                 54
  N1                8                 46
  N2                3                  8
  N3                0                  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                 M0 M1 M1A MX
  12Q LOSS MUTATED   17  1   1  3
  12Q LOSS WILD-TYPE 94  1   2 14
D64V6, multiclass
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                17                 94
  M1                 1                  1
  M1A                1                  2
  MX                 3                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     7  18
  12Q LOSS WILD-TYPE  14 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      7   18
  12Q LOSS WILD-TYPE   14  111
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                7                 14
  MALE                 18                111
[1] 2 2
[1] FALSE
D64V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       1                         1    19
  12Q LOSS WILD-TYPE    37                         1    74
D64V9, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    1                 37
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   19                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   33 17
  13Q LOSS WILD-TYPE 55 37
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                50                 92 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                17                 37 
$`13Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3QL 
       25.78        58.55         7.63         8.94        32.45        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
        0.85        20.78         0.26         0.53        17.03        23.41 
TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A93E TCGA-L5-A4OE 
        0.13        44.75        60.39        68.02        18.08         3.52 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A891 
        3.68         6.41         4.08         3.16        29.00         3.95 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K 
       13.22         5.42        13.41        83.24        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.45         0.07         0.33         0.10         0.13         0.07 
TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.07         0.13         0.07         0.10         0.10         0.10 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-VR-A8EU 
        0.07         0.20         5.06        29.59         6.35        18.31 
TCGA-VR-A8Q7 TCGA-VR-AA7I 
       36.72        15.91 

$`13Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30         5.92        13.94        16.24         4.21 
TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 
       33.27         2.63        20.12         0.03         0.99         0.79 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE 
        0.36        14.86         0.46         0.43       122.10         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        15.48        23.18        25.28 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       17.59         6.21         3.16         3.45         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO 
        8.94         3.35        19.50         8.78        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         1.38        30.74         4.90         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        6.94         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.02        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT 
       16.47        13.55         7.76        21.37         8.71        27.12 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
       52.57        46.09         0.16         0.10         0.10         0.07 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.07         0.07         0.10         1.18        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 
        3.78         8.02         7.59        14.70         7.04        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        9.30         7.00         8.78        14.01         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-AA4G 
        4.80         8.48         8.15         4.44         8.12        12.03 
TCGA-VR-AA7D TCGA-ZR-A9CJ 
        9.17        18.12 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.07               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             83.24             122.10 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             5.885              7.890 
[1] "0.1 - 83.2 (5.9)"  "0.0 - 122.1 (7.9)"
[1] "hr=" "1.2"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED         3        2        0        1        14         9
  13Q LOSS WILD-TYPE       5        2        6        0        21        17
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED          11          5          2          1        1
  13Q LOSS WILD-TYPE        12          6          6          5        2
                    vv
clus                 STAGE IVA
  13Q LOSS MUTATED           0
  13Q LOSS WILD-TYPE         2
D65V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  2                  2
  STAGE IB                  0                  6
  STAGE II                  1                  0
  STAGE IIA                14                 21
  STAGE IIB                 9                 17
  STAGE III                11                 12
  STAGE IIIA                5                  6
  STAGE IIIB                2                  6
  STAGE IIIC                1                  5
  STAGE IV                  1                  2
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  13Q LOSS MUTATED       8 11 28  3
  13Q LOSS WILD-TYPE    18 22 46  1
D65V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1                8                 18
  T2                  11                 22
  T3                  28                 46
  T4                   3                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  13Q LOSS MUTATED   26 21  2  1
  13Q LOSS WILD-TYPE 38 33  9  5
D65V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               26                 38
  N1               21                 33
  N2                2                  9
  N3                1                  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                 M0 M1 M1A MX
  13Q LOSS MUTATED   44  1   0  2
  13Q LOSS WILD-TYPE 67  1   3 15
D65V6, multiclass
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0                44                 67
  M1                 1                  1
  M1A                0                  3
  MX                 2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    4 49
  13Q LOSS WILD-TYPE 17 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4   49
  13Q LOSS WILD-TYPE   17   80
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                4                 17
  MALE                 49                 80
[1] 2 2
[1] FALSE
D65V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED      21                         0    27
  13Q LOSS WILD-TYPE    17                         2    66
D65V9, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                   21                 17
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   27                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   23 15
  14Q LOSS WILD-TYPE 65 39
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                38                104 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                15                 39 
$`14Q LOSS MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL 
        7.63         8.94        16.24         4.21        32.45        20.09 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB 
       23.41         0.36         0.46         0.43       122.10        60.39 
TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       42.77        18.08         0.30         8.94         3.52         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88Y TCGA-L5-A891 
        3.35        19.50         7.13         6.94         0.36         3.95 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49W 
       55.50         2.66        16.47        10.36        10.45         0.07 
TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO 
       17.62         7.59         5.06         6.35         9.30         7.00 
TCGA-VR-A8Q7 TCGA-VR-AA4G 
       36.72        12.03 

$`14Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27         0.85        20.78         2.63        20.12         0.03 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS 
        0.26         0.99         0.53        17.03         0.79         0.13 
TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 
       14.86        44.75        68.02         3.68        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       15.48        23.18        25.28        17.59         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.45         4.31         8.78         6.41         4.08        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        30.74         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.43         8.71         2.60        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
        3.02        35.97        12.92        13.48        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.42        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       83.24        52.57        46.09         0.07         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
        0.33         0.10         0.13         0.07         0.10         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.07         0.13         0.07         0.10         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.07         0.07         0.10         0.07         0.20         1.18 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        5.16         3.78         8.02        14.70         7.04        29.59 
TCGA-R6-A6Y0 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       53.95         8.78        14.01         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA7D 
        8.48         8.15         4.44        18.31         8.12         9.17 
TCGA-VR-AA7I TCGA-ZR-A9CJ 
       15.91        18.12 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.07               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            122.10              83.24 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             8.285              7.285 
[1] "0.1 - 122.1 (8.3)" "0.0 - 83.2 (7.3)" 
[1] "hr=" "1.1"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED         4        0        1        0         5         7
  14Q LOSS WILD-TYPE       4        4        5        1        30        19
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           6          3          3          1        0
  14Q LOSS WILD-TYPE        17          8          5          5        3
                    vv
clus                 STAGE IVA
  14Q LOSS MUTATED           2
  14Q LOSS WILD-TYPE         0
D66V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  0                  4
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 5                 30
  STAGE IIB                 7                 19
  STAGE III                 6                 17
  STAGE IIIA                3                  8
  STAGE IIIB                3                  5
  STAGE IIIC                1                  5
  STAGE IV                  0                  3
  STAGE IVA                 2                  0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  14Q LOSS MUTATED       8  6 21  0
  14Q LOSS WILD-TYPE    18 27 53  4
D66V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1                8                 18
  T2                   6                 27
  T3                  21                 53
  T4                   0                  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                 N0 N1 N2 N3
  14Q LOSS MUTATED   13 15  5  1
  14Q LOSS WILD-TYPE 51 39  6  5
D66V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               13                 51
  N1               15                 39
  N2                5                  6
  N3                1                  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                 M0 M1 M1A MX
  14Q LOSS MUTATED   27  0   2  4
  14Q LOSS WILD-TYPE 84  2   1 13
D66V6, multiclass
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0                27                 84
  M1                 0                  2
  M1A                2                  1
  MX                 4                 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"
D66V7, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    7 32
  14Q LOSS WILD-TYPE 14 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      7   32
  14Q LOSS WILD-TYPE   14   97
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                7                 14
  MALE                 32                 97
[1] 2 2
[1] FALSE
D66V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       6                         0    25
  14Q LOSS WILD-TYPE    32                         2    68
D66V9, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    6                 32
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   25                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   29 14
  15Q LOSS WILD-TYPE 59 40
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                43                 99 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                14                 40 
$`15Q LOSS MUTATED`
TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A4P3 
        5.92        16.24        32.45        20.09        20.12         0.03 
TCGA-IG-A4QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D 
        0.26         0.46         0.43        25.41        23.18        25.28 
TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH 
       18.08         0.30         8.94         3.52         3.35        19.50 
TCGA-L5-A4OM TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        4.08         4.90        29.00         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       35.97        12.92        13.48         5.42         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 
       27.12        83.24         0.10         0.10         0.20         1.18 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RE TCGA-VR-A8EU 
        5.06        29.59         7.00         8.78         4.80        18.31 
TCGA-ZR-A9CJ 
       18.12 

$`15Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        8.94         4.21        33.27         0.85        20.78         2.63 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        0.99         0.53        17.03         0.79        23.41         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.13        14.86       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93F TCGA-KH-A6WC 
        3.68        41.52        42.77        15.48        17.59         6.21 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.16         3.45         4.31         3.68         8.78         6.41 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        30.74 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        0.36         7.40         3.95        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
        7.76        21.37        52.57        46.09        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45         0.16         0.07         0.33         0.10         0.13 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        0.07         0.10         0.07         0.10         0.07         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR 
        0.07         0.10         0.10         0.07         0.07         0.07 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       17.62         5.16         3.78         8.02         7.59        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BW TCGA-V5-A7RB 
        7.04         6.35        53.95         9.30        14.01         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-A8Q7 
        3.42         8.48         8.15         4.44         8.12        36.72 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       12.03         9.17        15.91 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.03               0.07 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             83.24             122.10 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              8.78               7.40 
[1] "0.0 - 83.2 (8.8)"  "0.1 - 122.1 (7.4)"
[1] "hr=" "1.4"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED         3        1        1        0         7         8
  15Q LOSS WILD-TYPE       5        3        5        1        28        18
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED           8          3          4          2        3
  15Q LOSS WILD-TYPE        15          8          4          4        0
                    vv
clus                 STAGE IVA
  15Q LOSS MUTATED           2
  15Q LOSS WILD-TYPE         0
D67V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  1                  3
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 7                 28
  STAGE IIB                 8                 18
  STAGE III                 8                 15
  STAGE IIIA                3                  8
  STAGE IIIB                4                  4
  STAGE IIIC                2                  4
  STAGE IV                  3                  0
  STAGE IVA                 2                  0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  15Q LOSS MUTATED       9  7 27  0
  15Q LOSS WILD-TYPE    17 26 47  4
D67V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1                9                 17
  T2                   7                 26
  T3                  27                 47
  T4                   0                  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                 N0 N1 N2 N3
  15Q LOSS MUTATED   17 18  5  2
  15Q LOSS WILD-TYPE 47 36  6  4
D67V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               17                 47
  N1               18                 36
  N2                5                  6
  N3                2                  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                 M0 M1 M1A MX
  15Q LOSS MUTATED   33  2   3  3
  15Q LOSS WILD-TYPE 78  0   0 14
D67V6, multiclass
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0                33                 78
  M1                 2                  0
  M1A                3                  0
  MX                 3                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    6 39
  15Q LOSS WILD-TYPE 15 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      6   39
  15Q LOSS WILD-TYPE   15   90
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                6                 15
  MALE                 39                 90
[1] 2 2
[1] FALSE
D67V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       9                         0    31
  15Q LOSS WILD-TYPE    29                         2    62
D67V9, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    9                 29
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   31                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED   25 19
  16P LOSS WILD-TYPE 63 35
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                44                 98 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                19                 35 
$`16P LOSS MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3YC 
        7.63         5.92        13.94         8.94        32.45        20.12 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OE 
       42.77        25.41        23.18        18.08         3.16         3.52 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.35        19.50         6.41         3.16        30.74         4.90 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NN 
        0.36         7.40         3.95         3.02        12.92         5.42 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       83.24        52.57        46.09        10.45         0.07         0.33 
TCGA-LN-A49V TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6XQ 
        0.10         0.10         0.10         5.16         8.02         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       53.95         9.30         7.00         5.29         3.42         4.80 
TCGA-V5-AASW TCGA-VR-A8Q7 
        8.15        36.72 

$`16P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        31.27        14.30        58.55        16.24         4.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 
       33.27        20.09         0.85        20.78         2.63         0.03 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        0.26         0.99         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
        0.36         0.13        14.86         0.46         0.43       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       44.75        60.39        68.02         3.68        41.52        15.48 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       25.28        17.59         6.21         3.45         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        8.94         3.68         8.78         4.08        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        7.17         1.38        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        8.71         2.60        25.12        55.50         2.66        35.97 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
        8.71        13.41        27.12        10.36         0.07         0.16 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.10         0.13         0.07         0.07         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.13         0.07         0.10         0.10         0.07         0.07 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ 
        0.07         0.20         1.18        17.62         3.78         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-S8-A6BV TCGA-S8-A6BW 
        5.06        14.70         7.04        29.59         8.78        14.01 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D 
        8.48         4.44        18.31         8.12        12.03         9.17 
TCGA-VR-AA7I TCGA-ZR-A9CJ 
       15.91        18.12 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.07               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             83.24             122.10 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             7.200              7.675 
[1] "0.1 - 83.2 (7.2)"  "0.0 - 122.1 (7.7)"
[1] "hr=" "1.1"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P LOSS MUTATED         4        1        2        0         9         6
  16P LOSS WILD-TYPE       4        3        4        1        26        20
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED           5          3          3          0        2
  16P LOSS WILD-TYPE        18          8          5          6        1
                    vv
clus                 STAGE IVA
  16P LOSS MUTATED           0
  16P LOSS WILD-TYPE         2
D68V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  1                  3
  STAGE IB                  2                  4
  STAGE II                  0                  1
  STAGE IIA                 9                 26
  STAGE IIB                 6                 20
  STAGE III                 5                 18
  STAGE IIIA                3                  8
  STAGE IIIB                3                  5
  STAGE IIIC                0                  6
  STAGE IV                  2                  1
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  16P LOSS MUTATED      12  8 18  0
  16P LOSS WILD-TYPE    14 25 56  4
D68V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1               12                 14
  T2                   8                 25
  T3                  18                 56
  T4                   0                  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                 N0 N1 N2 N3
  16P LOSS MUTATED   17 18  3  0
  16P LOSS WILD-TYPE 47 36  8  6
D68V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               17                 47
  N1               18                 36
  N2                3                  8
  N3                0                  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                 M0 M1 M1A MX
  16P LOSS MUTATED   32  1   1  3
  16P LOSS WILD-TYPE 79  1   2 14
D68V6, multiclass
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0                32                 79
  M1                 1                  1
  M1A                1                  2
  MX                 3                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    7 38
  16P LOSS WILD-TYPE 14 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7   38
  16P LOSS WILD-TYPE   14   91
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                7                 14
  MALE                 38                 91
[1] 2 2
[1] FALSE
D68V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       8                         1    30
  16P LOSS WILD-TYPE    30                         1    63
D68V9, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    8                 30
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   30                 63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   26 17
  16Q LOSS WILD-TYPE 62 37
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                43                 99 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                17                 37 
$`16Q LOSS MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       31.27         7.63         5.92         8.94        16.24        32.45 
TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A97H TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C 
       20.09        20.12         0.43        42.77        25.41        23.18 
TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16         8.94         3.52         3.35        19.50         6.41 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
        3.16        30.74         4.90         0.36         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
       55.50         5.42         8.71        83.24        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A4MQ TCGA-Q9-A6FU TCGA-R6-A6KZ 
       10.45         0.33         0.10         0.10         5.16         5.06 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
        6.35        53.95         9.30         7.00         5.29         4.80 
TCGA-V5-AASW 
        8.15 

$`16Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 
       25.78        14.30        58.55        13.94         4.21        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63         0.03         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86         0.46       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
        3.68        41.52        15.48        25.28        18.08        17.59 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OI 
        6.21         3.45         0.30         4.31         3.68         8.78 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OU 
        4.08        18.35         3.32         7.17         1.38        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        7.40         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT 
       13.55        13.22         7.76        21.37        13.41        27.12 
TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S 
       52.57         0.07         0.16         0.07         0.10         0.13 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.07         0.07         0.10         0.07         0.13         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR 
        0.10         0.10         0.10         0.07         0.07         0.07 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.20         1.18        17.62         3.78         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC 
       14.70         7.04        29.59         8.78        14.01         3.42 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.48         4.44        18.31         8.12        36.72        12.03 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        9.17        15.91        18.12 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.10               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             83.24             122.10 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              7.63               7.43 
[1] "0.1 - 83.2 (7.6)"  "0.0 - 122.1 (7.4)"
[1] "hr=" "1.1"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q LOSS MUTATED         4        1        2        0         7         7
  16Q LOSS WILD-TYPE       4        3        4        1        28        19
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED           6          1          3          1        1
  16Q LOSS WILD-TYPE        17         10          5          5        2
                    vv
clus                 STAGE IVA
  16Q LOSS MUTATED           1
  16Q LOSS WILD-TYPE         1
D69V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  1                  3
  STAGE IB                  2                  4
  STAGE II                  0                  1
  STAGE IIA                 7                 28
  STAGE IIB                 7                 19
  STAGE III                 6                 17
  STAGE IIIA                1                 10
  STAGE IIIB                3                  5
  STAGE IIIC                1                  5
  STAGE IV                  1                  2
  STAGE IVA                 1                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  16Q LOSS MUTATED      10  7 21  0
  16Q LOSS WILD-TYPE    16 26 53  4
D69V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1               10                 16
  T2                   7                 26
  T3                  21                 53
  T4                   0                  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                 N0 N1 N2 N3
  16Q LOSS MUTATED   15 17  4  1
  16Q LOSS WILD-TYPE 49 37  7  5
D69V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               15                 49
  N1               17                 37
  N2                4                  7
  N3                1                  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                 M0 M1 M1A MX
  16Q LOSS MUTATED   30  0   2  5
  16Q LOSS WILD-TYPE 81  2   1 12
D69V6, multiclass
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0                30                 81
  M1                 0                  2
  M1A                2                  1
  MX                 5                 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"
D69V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    8 36
  16Q LOSS WILD-TYPE 13 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      8   36
  16Q LOSS WILD-TYPE   13   93
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                8                 13
  MALE                 36                 93
[1] 2 2
[1] FALSE
D69V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       7                         0    28
  16Q LOSS WILD-TYPE    31                         2    65
D69V9, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    7                 31
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   28                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   34 21
  17P LOSS WILD-TYPE 54 33
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                55                 87 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                21                 33 
$`17P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR 
       25.78         7.63         5.92         8.94         4.21        32.45 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6F8 
        0.03         0.26         0.79        23.41         0.43       122.10 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF 
       42.77        25.41        25.28         3.45         3.52         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OW 
        3.35        19.50         3.32         7.17         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NL 
        7.43         2.60         0.36         3.95        16.47        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49K 
        5.42         8.71        13.41        27.12        83.24         0.07 
TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU 
       10.45         0.13         0.07         0.20        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-RE-A7BO 
        3.78         7.59         7.04        29.59         9.30         7.00 
TCGA-S8-A6BV TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EW 
        8.78         4.80         8.48         8.15         4.44         8.12 
TCGA-VR-A8Q7 
       36.72 

$`17P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IG-A3I8 
       31.27        14.30        58.55        13.94        16.24        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT 
       20.09         0.85        20.78         2.63        20.12         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.53        17.03         0.36         0.13        14.86         0.46 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       44.75        60.39        68.02         3.68        41.52        15.48 
TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       23.18        18.08        17.59         6.21         3.16         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        4.31         8.94         8.78         6.41         4.08        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T 
        1.38         3.16        30.74        29.00         6.94         8.71 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
       25.12         7.40         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NV 
       12.92        13.48        13.55         7.76        21.37        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       46.09        10.36         0.16         0.07         0.33         0.10 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.07         0.10         0.10         0.07         0.13         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10         0.10         0.10         0.07         0.07         0.10 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XQ 
        0.07         1.18         8.02         5.06        14.70         6.35 
TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-VR-A8EU TCGA-VR-AA4G 
       53.95        14.01         5.29         3.42        18.31        12.03 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
        9.17        15.91        18.12 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.03               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            122.10              68.02 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              7.17               8.02 
[1] "0.0 - 122.1 (7.2)" "0.1 - 68.0 (8.0)" 
[1] "hr=" "1.1"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED         4        1        2        0        10        12
  17P LOSS WILD-TYPE       4        3        4        1        25        14
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED          11          2          5          2        1
  17P LOSS WILD-TYPE        12          9          3          4        2
                    vv
clus                 STAGE IVA
  17P LOSS MUTATED           0
  17P LOSS WILD-TYPE         2
D70V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   4                  4
  STAGE IA                  1                  3
  STAGE IB                  2                  4
  STAGE II                  0                  1
  STAGE IIA                10                 25
  STAGE IIB                12                 14
  STAGE III                11                 12
  STAGE IIIA                2                  9
  STAGE IIIB                5                  3
  STAGE IIIC                2                  4
  STAGE IV                  1                  2
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  17P LOSS MUTATED       9 10 33  0
  17P LOSS WILD-TYPE    17 23 41  4
D70V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1                9                 17
  T2                  10                 23
  T3                  33                 41
  T4                   0                  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                 N0 N1 N2 N3
  17P LOSS MUTATED   22 22  5  2
  17P LOSS WILD-TYPE 42 32  6  4
D70V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               22                 42
  N1               22                 32
  N2                5                  6
  N3                2                  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                 M0 M1 M1A MX
  17P LOSS MUTATED   44  0   1  5
  17P LOSS WILD-TYPE 67  2   2 12
D70V6, multiclass
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0                44                 67
  M1                 0                  2
  M1A                1                  2
  MX                 5                 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"
D70V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    8 50
  17P LOSS WILD-TYPE 13 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      8   50
  17P LOSS WILD-TYPE   13   79
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                8                 13
  MALE                 50                 79
[1] 2 2
[1] FALSE
D70V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED      10                         1    38
  17P LOSS WILD-TYPE    28                         1    55
D70V9, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                   10                 28
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   38                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    9  7
  17Q LOSS WILD-TYPE 79 47
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                16                126 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 7                 47 
$`17Q LOSS MUTATED`
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A938 
        8.94         4.21         0.79        23.41         0.43        25.41 
TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A891 TCGA-LN-A49L TCGA-LN-A5U6 TCGA-Q9-A6FU 
        7.13         0.36         3.95        10.45         0.20         5.16 
TCGA-R6-A6Y2 TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8Q7 
        9.30         4.80         4.44        36.72 

$`17Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       13.94        16.24        32.45        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12         0.03         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.53        17.03         0.36         0.13        14.86         0.46 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
      122.10        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       42.77        15.48        23.18        25.28        18.08        17.59 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
        6.21         3.16         3.45         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.52         3.68         3.35        19.50         8.78         6.41 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
        4.08        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
       30.74         4.90        29.00         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.42        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
       83.24        52.57        46.09        10.36         0.07         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
        0.07         0.33         0.10         0.13         0.07         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.07         0.10         0.07         0.13         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.10         0.10         0.07         0.07         0.10         0.07 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        1.18        17.62         3.78         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-RE-A7BO 
       14.70         7.04        29.59         6.35        53.95         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW 
        8.78        14.01         5.29         3.42         8.48         8.15 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
       18.31         8.12        12.03         9.17        15.91        18.12 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.20               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             36.72             122.10 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             4.980              7.695 
[1] "0.2 - 36.7 (5.0)"  "0.0 - 122.1 (7.7)"
[1] "hr=" "1.7"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED         0        0        2        0         3         4
  17Q LOSS WILD-TYPE       8        4        4        1        32        22
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED           2          1          1          0        0
  17Q LOSS WILD-TYPE        21         10          7          6        3
                    vv
clus                 STAGE IVA
  17Q LOSS MUTATED           0
  17Q LOSS WILD-TYPE         2
D71V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  0                  4
  STAGE IB                  2                  4
  STAGE II                  0                  1
  STAGE IIA                 3                 32
  STAGE IIB                 4                 22
  STAGE III                 2                 21
  STAGE IIIA                1                 10
  STAGE IIIB                1                  7
  STAGE IIIC                0                  6
  STAGE IV                  0                  3
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  17Q LOSS MUTATED       2  3 10  0
  17Q LOSS WILD-TYPE    24 30 64  4
D71V4, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1                2                 24
  T2                   3                 30
  T3                  10                 64
  T4                   0                  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                 N0 N1 N2 N3
  17Q LOSS MUTATED    7  6  1  0
  17Q LOSS WILD-TYPE 57 48 10  6
D71V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                7                 57
  N1                6                 48
  N2                1                 10
  N3                0                  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                 M0 M1 M1A MX
  17Q LOSS MUTATED   14  0   0  1
  17Q LOSS WILD-TYPE 97  2   3 16
D71V6, multiclass
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                14                 97
  M1                 0                  2
  M1A                0                  3
  MX                 1                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     3  14
  17Q LOSS WILD-TYPE  18 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3   14
  17Q LOSS WILD-TYPE   18  115
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                3                 18
  MALE                 14                115
[1] 2 2
[1] FALSE
D71V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       4                         0    10
  17Q LOSS WILD-TYPE    34                         2    83
D71V9, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    4                 34
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   10                 83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   34 25
  18P LOSS WILD-TYPE 54 29
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                59                 83 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                25                 29 
$`18P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78        14.30         5.92         8.94        16.24        32.45 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H 
       33.27         0.85         2.63         0.79        23.41         0.43 
TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       44.75        42.77        23.18        25.28        18.08        17.59 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.16         3.45         0.30         8.94         3.52         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        3.35        19.50         7.17         7.43         6.94         2.60 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.95        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K 
       16.47        13.55         8.71        52.57        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ 
       10.45         0.07         0.33         5.16         3.78         7.59 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
       29.59         6.35        53.95         9.30         7.00         8.78 
TCGA-V5-A7RB TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8EW TCGA-ZR-A9CJ 
        5.29         8.15        18.31         8.12        18.12 

$`18P LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3QL 
       31.27        58.55         7.63        13.94         4.21        20.09 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78        20.12         0.03         0.26         0.99         0.53 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 
       17.03         0.36         0.13        14.86         0.46       122.10 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 
       60.39        68.02         3.68        41.52        25.41        15.48 
TCGA-KH-A6WC TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        6.21         4.31         8.78         6.41         4.08        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         1.38         3.16        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 
        7.13         8.71        25.12         0.36         7.40         3.02 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT 
       13.22         7.76         5.42        21.37        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       83.24        46.09         0.16         0.10         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10         0.07         0.10         0.07         0.13         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10         0.10         0.10         0.07         0.07         0.10 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ 
        0.07         0.20         1.18        17.62         8.02         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       14.70         7.04        14.01         3.42         4.80         8.48 
TCGA-V5-AASX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        4.44        36.72        12.03         9.17        15.91 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.07               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              55.5              122.1 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              8.78               6.21 
[1] "0.1 - 55.5 (8.8)"  "0.0 - 122.1 (6.2)"
[1] "hr=" "1.1"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED         3        1        3        0        10         8
  18P LOSS WILD-TYPE       5        3        3        1        25        18
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED          11          4          5          3        2
  18P LOSS WILD-TYPE        12          7          3          3        1
                    vv
clus                 STAGE IVA
  18P LOSS MUTATED           2
  18P LOSS WILD-TYPE         0
D72V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  1                  3
  STAGE IB                  3                  3
  STAGE II                  0                  1
  STAGE IIA                10                 25
  STAGE IIB                 8                 18
  STAGE III                11                 12
  STAGE IIIA                4                  7
  STAGE IIIB                5                  3
  STAGE IIIC                3                  3
  STAGE IV                  2                  1
  STAGE IVA                 2                  0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  18P LOSS MUTATED      10  8 36  1
  18P LOSS WILD-TYPE    16 25 38  3
D72V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1               10                 16
  T2                   8                 25
  T3                  36                 38
  T4                   1                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  18P LOSS MUTATED   20 25  6  3
  18P LOSS WILD-TYPE 44 29  5  3
D72V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               20                 44
  N1               25                 29
  N2                6                  5
  N3                3                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  18P LOSS MUTATED   41  2   2  8
  18P LOSS WILD-TYPE 70  0   1  9
D72V6, multiclass
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0                41                 70
  M1                 2                  0
  M1A                2                  1
  MX                 8                  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"
D72V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   11 51
  18P LOSS WILD-TYPE 10 78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     11   51
  18P LOSS WILD-TYPE   10   78
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               11                 10
  MALE                 51                 78
[1] 2 2
[1] FALSE
D72V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED      11                         0    42
  18P LOSS WILD-TYPE    27                         2    51
D72V9, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                   11                 27
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   42                 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"

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   50 30
  18Q LOSS WILD-TYPE 38 24
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                80                 62 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                30                 24 
$`18Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78        31.27        14.30         8.94        16.24        32.45 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 
        0.85         2.63         0.26         0.53         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FH TCGA-JY-A938 
        0.13         0.43        44.75        68.02        42.77        25.41 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43H 
       23.18        25.28        18.08        17.59         3.16         0.30 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO 
        8.94         3.52         3.68         3.35        19.50         3.32 
TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        7.17         4.90        29.00         7.43         6.94         2.60 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       13.48        16.47        13.55         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       83.24        52.57        10.36        10.45         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ 
        0.33         0.10         0.07         0.10         0.10         0.10 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.07         0.20        17.62         5.16         3.78         8.02 
TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BV 
        7.59        29.59         6.35        53.95         7.00         8.78 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G 
        5.29         3.42         8.15        18.31         8.12        12.03 
TCGA-VR-AA7D TCGA-ZR-A9CJ 
        9.17        18.12 

$`18Q LOSS WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 
       58.55         7.63         5.92        13.94         4.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D 
       20.09        20.78        20.12         0.03         0.99        17.03 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE 
        0.36        14.86         0.46       122.10        60.39         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OI 
       41.52        15.48         6.21         3.45         4.31         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        6.41         4.08        18.35         1.38         3.16        30.74 
TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NL 
        7.13         8.71        25.12         0.36         7.40        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49S 
        7.76         5.42        21.37        46.09         0.07         0.13 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.07         0.10         0.10         0.07         0.13         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.10         0.07         0.07         1.18         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        7.04         9.30        14.01         4.80         8.48         4.44 
TCGA-VR-A8Q7 TCGA-VR-AA7I 
       36.72        15.91 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.07               0.03 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             83.24             122.10 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             8.135              6.725 
[1] "0.1 - 83.2 (8.1)"  "0.0 - 122.1 (6.7)"
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED         3        1        3        1        17        14
  18Q LOSS WILD-TYPE       5        3        3        0        18        12
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED          12          6          6          5        3
  18Q LOSS WILD-TYPE        11          5          2          1        0
                    vv
clus                 STAGE IVA
  18Q LOSS MUTATED           2
  18Q LOSS WILD-TYPE         0
D73V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   3                  5
  STAGE IA                  1                  3
  STAGE IB                  3                  3
  STAGE II                  1                  0
  STAGE IIA                17                 18
  STAGE IIB                14                 12
  STAGE III                12                 11
  STAGE IIIA                6                  5
  STAGE IIIB                6                  2
  STAGE IIIC                5                  1
  STAGE IV                  3                  0
  STAGE IVA                 2                  0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  18Q LOSS MUTATED      11 18 46  1
  18Q LOSS WILD-TYPE    15 15 28  3
D73V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1               11                 15
  T2                  18                 15
  T3                  46                 28
  T4                   1                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  18Q LOSS MUTATED   31 31  8  5
  18Q LOSS WILD-TYPE 33 23  3  1
D73V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               31                 33
  N1               31                 23
  N2                8                  3
  N3                5                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  18Q LOSS MUTATED   61  2   3  8
  18Q LOSS WILD-TYPE 50  0   0  9
D73V6, multiclass
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0                61                 50
  M1                 2                  0
  M1A                3                  0
  MX                 8                  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"
D73V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   13 71
  18Q LOSS WILD-TYPE  8 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     13   71
  18Q LOSS WILD-TYPE    8   58
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               13                  8
  MALE                 71                 58
[1] 2 2
[1] FALSE
D73V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED      20                         1    52
  18Q LOSS WILD-TYPE    18                         1    41
D73V9, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                   20                 18
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   52                 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"

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED   32 19
  19P LOSS WILD-TYPE 56 35
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                51                 91 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                19                 35 
$`19P LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        31.27        14.30         7.63        16.24         4.21 
TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS 
        2.63         0.26         0.53        17.03        23.41         0.13 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FH TCGA-L5-A43E TCGA-L5-A43J 
        0.43       122.10        68.02        42.77         3.45         4.31 
TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88V 
        3.68         4.08         7.17        30.74         7.43         2.60 
TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
        3.95         2.66        16.47        13.55        13.22         5.42 
TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R 
        8.71        52.57        46.09        10.45         0.16         0.10 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
        0.07         0.07         0.07         0.13         0.07         0.10 
TCGA-LN-A5U6 TCGA-R6-A6DN TCGA-R6-A6L6 TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EW 
        0.20         8.02         7.04         3.42         8.15         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA7D TCGA-ZR-A9CJ 
       36.72         9.17        18.12 

$`19P LOSS WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3I8 
       58.55         5.92        13.94         8.94        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
       20.09         0.85        20.78        20.12         0.03         0.99 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB 
        0.79         0.36        14.86         0.46        44.75        60.39 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        25.41        15.48        23.18        25.28 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M 
       18.08        17.59         6.21         3.16         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
        3.52         3.35        19.50         8.78         6.41        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        3.32         1.38         3.16         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 
        6.94         8.71        25.12         0.36         7.40         3.02 
TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ 
       55.50        35.97        12.92        13.48         7.76        21.37 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N 
       13.41        27.12        83.24        10.36         0.07         0.07 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.33         0.13         0.10         0.10         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 
        0.07         0.07         0.10         0.07         1.18        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
        5.16         3.78         7.59         5.06        14.70        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        6.35        53.95         9.30         7.00         8.78        14.01 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-AA4G 
        5.29         4.80         8.48         4.44        18.31        12.03 
TCGA-VR-AA7I 
       15.91 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.07               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            122.10              83.24 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              7.17               7.76 
[1] "0.1 - 122.1 (7.2)" "0.0 - 83.2 (7.8)" 
[1] "hr=" "1"  
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED         2        2        1        1        12        10
  19P LOSS WILD-TYPE       6        2        5        0        23        16
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED          12          3          2          2        0
  19P LOSS WILD-TYPE        11          8          6          4        3
                    vv
clus                 STAGE IVA
  19P LOSS MUTATED           2
  19P LOSS WILD-TYPE         0
D74V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  2                  2
  STAGE IB                  1                  5
  STAGE II                  1                  0
  STAGE IIA                12                 23
  STAGE IIB                10                 16
  STAGE III                12                 11
  STAGE IIIA                3                  8
  STAGE IIIB                2                  6
  STAGE IIIC                2                  4
  STAGE IV                  0                  3
  STAGE IVA                 2                  0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  19P LOSS MUTATED       8 11 31  0
  19P LOSS WILD-TYPE    18 22 43  4
D74V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1                8                 18
  T2                  11                 22
  T3                  31                 43
  T4                   0                  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                 N0 N1 N2 N3
  19P LOSS MUTATED   19 26  2  2
  19P LOSS WILD-TYPE 45 28  9  4
D74V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               19                 45
  N1               26                 28
  N2                2                  9
  N3                2                  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                 M0 M1 M1A MX
  19P LOSS MUTATED   42  0   2  4
  19P LOSS WILD-TYPE 69  2   1 13
D74V6, multiclass
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0                42                 69
  M1                 0                  2
  M1A                2                  1
  MX                 4                 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"
D74V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    7 47
  19P LOSS WILD-TYPE 14 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      7   47
  19P LOSS WILD-TYPE   14   82
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                7                 14
  MALE                 47                 82
[1] 2 2
[1] FALSE
D74V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED      17                         1    28
  19P LOSS WILD-TYPE    21                         1    65
D74V9, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                   17                 21
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   28                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED   25 13
  19Q LOSS WILD-TYPE 63 41
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                38                104 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                13                 41 
$`19Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GQ TCGA-IG-A3YB TCGA-IG-A50L 
       25.78        31.27        14.30         4.21         2.63         0.53 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FH 
       23.41         0.13         0.43       122.10        68.02        42.77 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OX 
        3.45         4.31         4.08         7.17        30.74         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NL TCGA-L5-A8NR 
        6.94         2.60         3.95         2.66        13.22         8.71 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y 
       10.45         0.16         0.10         0.13         0.07         0.07 
TCGA-LN-A4A2 TCGA-LN-A5U6 TCGA-R6-A6DN TCGA-V5-A7RC TCGA-VR-A8EW TCGA-VR-A8Q7 
        0.13         0.20         8.02         3.42         8.12        36.72 
TCGA-VR-AA7D TCGA-ZR-A9CJ 
        9.17        18.12 

$`19Q LOSS WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
       32.45        33.27        20.09         0.85        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
        0.03         0.26         0.99        17.03         0.79         0.36 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG 
       14.86         0.46        44.75        60.39         3.68        41.52 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        15.48        23.18        25.28        18.08        17.59 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        6.21         3.16         0.30         8.94         3.52         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO 
        3.35        19.50         8.78         6.41        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88T 
        1.38         3.16         4.90        29.00         7.13         8.71 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG 
       25.12         0.36         7.40         3.02        55.50        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55         7.76         5.42 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37        13.41        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V 
       10.36         0.07         0.07         0.33         0.07         0.10 
TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.10         0.07         0.10         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.07         0.10         0.07         1.18        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        3.78         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        6.35        53.95         9.30         7.00         8.78        14.01 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU 
        5.29         4.80         8.48         8.15         4.44        18.31 
TCGA-VR-AA4G TCGA-VR-AA7I 
       12.03        15.91 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.07               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            122.10              83.24 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             5.625              7.955 
[1] "0.1 - 122.1 (5.6)" "0.0 - 83.2 (8.0)" 
[1] "hr=" "1"  
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED         2        2        1        0        10         8
  19Q LOSS WILD-TYPE       6        2        5        1        25        18
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED           8          3          1          2        0
  19Q LOSS WILD-TYPE        15          8          7          4        3
                    vv
clus                 STAGE IVA
  19Q LOSS MUTATED           1
  19Q LOSS WILD-TYPE         1
D75V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   2                  6
  STAGE IA                  2                  2
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                10                 25
  STAGE IIB                 8                 18
  STAGE III                 8                 15
  STAGE IIIA                3                  8
  STAGE IIIB                1                  7
  STAGE IIIC                2                  4
  STAGE IV                  0                  3
  STAGE IVA                 1                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  19Q LOSS MUTATED       6  9 24  0
  19Q LOSS WILD-TYPE    20 24 50  4
D75V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1                6                 20
  T2                   9                 24
  T3                  24                 50
  T4                   0                  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                 N0 N1 N2 N3
  19Q LOSS MUTATED   17 18  1  2
  19Q LOSS WILD-TYPE 47 36 10  4
D75V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               17                 47
  N1               18                 36
  N2                1                 10
  N3                2                  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                 M0 M1 M1A MX
  19Q LOSS MUTATED   32  0   1  5
  19Q LOSS WILD-TYPE 79  2   2 12
D75V6, multiclass
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                32                 79
  M1                 0                  2
  M1A                1                  2
  MX                 5                 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"
D75V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    6 35
  19Q LOSS WILD-TYPE 15 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6   35
  19Q LOSS WILD-TYPE   15   94
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                6                 15
  MALE                 35                 94
[1] 2 2
[1] FALSE
D75V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED      15                         1    19
  19Q LOSS WILD-TYPE    23                         1    74
D75V9, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                   15                 23
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   19                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED   12  3
  20P LOSS WILD-TYPE 76 51
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                15                127 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                 51 
$`20P LOSS MUTATED`
TCGA-2H-A9GI TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FH TCGA-L5-A43M TCGA-L5-A4OF 
       14.30        44.75        68.02        42.77         8.94         3.68 
TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A8NL TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49O 
       19.50         3.32        13.22        83.24         0.16         0.33 
TCGA-LN-A49Y TCGA-R6-A6XG TCGA-S8-A6BW 
        0.07        29.59        14.01 

$`20P LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12         0.03         0.26 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        0.99         0.53        17.03         0.79        23.41         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB 
        0.13        14.86         0.46         0.43       122.10        60.39 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        25.41        15.48        23.18        25.28 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       18.08        17.59         6.21         3.16         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        4.31         3.52         3.35         8.78         6.41         4.08 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         7.17         1.38         3.16        30.74         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        2.66        35.97        12.92        13.48        16.47        13.55 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.42        21.37         8.71        13.41        27.12 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
       52.57        46.09        10.36         0.07        10.45         0.07 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10         0.13         0.07         0.10         0.07         0.10 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.13         0.07         0.10         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 
        0.07         0.10         0.07         0.20         1.18        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        5.16         3.78         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
        7.04         6.35        53.95         9.30         7.00         8.78 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42         4.80         8.48         8.15         4.44 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       18.31         8.12        36.72        12.03         9.17        15.91 
TCGA-ZR-A9CJ 
       18.12 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.07               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             83.24             122.10 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             14.01               7.17 
[1] "0.1 - 83.2 (14.0)" "0.0 - 122.1 (7.2)"
[1] "hr=" "3.4"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         1        0        1        0         6         3
  20P LOSS WILD-TYPE       7        4        5        1        29        23
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           3          0          0          1        0
  20P LOSS WILD-TYPE        20         11          8          5        3
                    vv
clus                 STAGE IVA
  20P LOSS MUTATED           0
  20P LOSS WILD-TYPE         2
D76V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  0                  4
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 6                 29
  STAGE IIB                 3                 23
  STAGE III                 3                 20
  STAGE IIIA                0                 11
  STAGE IIIB                0                  8
  STAGE IIIC                1                  5
  STAGE IV                  0                  3
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  20P LOSS MUTATED       2  6  8  0
  20P LOSS WILD-TYPE    24 27 66  4
D76V4, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1                2                 24
  T2                   6                 27
  T3                   8                 66
  T4                   0                  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                 N0 N1 N2 N3
  20P LOSS MUTATED    8  6  1  1
  20P LOSS WILD-TYPE 56 48 10  5
D76V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                8                 56
  N1                6                 48
  N2                1                 10
  N3                1                  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                 M0 M1 M1A MX
  20P LOSS MUTATED   13  0   0  2
  20P LOSS WILD-TYPE 98  2   3 15
D76V6, multiclass
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                13                 98
  M1                 0                  2
  M1A                0                  3
  MX                 2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     2  15
  20P LOSS WILD-TYPE  19 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   15
  20P LOSS WILD-TYPE   19  114
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                2                 19
  MALE                 15                114
[1] 2 2
[1] FALSE
D76V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       7                         0     8
  20P LOSS WILD-TYPE    31                         2    85
D76V9, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    7                 31
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    8                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                 0  1
  20Q LOSS MUTATED    4  1
  20Q LOSS WILD-TYPE 84 53
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 5                137 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 53 
$`20Q LOSS MUTATED`
TCGA-JY-A6FA TCGA-JY-A6FH TCGA-L5-A43M TCGA-L5-A4OO TCGA-S8-A6BW 
       44.75        42.77         8.94         3.32        14.01 

$`20Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12         0.03 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        0.26         0.99         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
        0.36         0.13        14.86         0.46         0.43       122.10 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 
       60.39        68.02         3.68        41.52        25.41        15.48 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        25.28        18.08        17.59         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.45         0.30         4.31         3.52         3.68         3.35 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
       19.50         8.78         6.41         4.08        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        30.74         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.43         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        7.40         3.95         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        5.42        21.37         8.71        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.36         0.07        10.45         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
        0.07         0.33         0.10         0.13         0.07         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.07         0.10         0.07         0.13         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.10         0.10         0.07         0.07         0.10         0.07 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.20         1.18        17.62         5.16         3.78         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC 
       53.95         9.30         7.00         8.78         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW 
        4.80         8.48         8.15         4.44        18.31         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
       36.72        12.03         9.17        15.91        18.12 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              3.32               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             44.75             122.10 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             14.01               7.40 
[1] "3.3 - 44.8 (14.0)" "0.0 - 122.1 (7.4)"
[1] "hr=" "3"  
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q LOSS MUTATED         0        0        1        0         1         2
  20Q LOSS WILD-TYPE       8        4        5        1        34        24
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED           0          0          0          1        0
  20Q LOSS WILD-TYPE        23         11          8          5        3
                    vv
clus                 STAGE IVA
  20Q LOSS MUTATED           0
  20Q LOSS WILD-TYPE         2
D77V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  0                  4
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 1                 34
  STAGE IIB                 2                 24
  STAGE III                 0                 23
  STAGE IIIA                0                 11
  STAGE IIIB                0                  8
  STAGE IIIC                1                  5
  STAGE IV                  0                  3
  STAGE IVA                 0                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  20Q LOSS MUTATED       0  4  2  0
  20Q LOSS WILD-TYPE    26 29 72  4
D77V4, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1                0                 26
  T2                   4                 29
  T3                   2                 72
  T4                   0                  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                 N0 N1 N2 N3
  20Q LOSS MUTATED    2  2  1  1
  20Q LOSS WILD-TYPE 62 52 10  5
D77V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                2                 62
  N1                2                 52
  N2                1                 10
  N3                1                  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                  M0  M1 M1A  MX
  20Q LOSS MUTATED     4   0   0   2
  20Q LOSS WILD-TYPE 107   2   3  15
D77V6, multiclass
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                 4                107
  M1                 0                  2
  M1A                0                  3
  MX                 2                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   5
  20Q LOSS WILD-TYPE  20 124
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    5
  20Q LOSS WILD-TYPE   20  124
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                1                 20
  MALE                  5                124
[1] 2 2
[1] FALSE
D77V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       2                         0     3
  20Q LOSS WILD-TYPE    36                         2    90
D77V9, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    2                 36
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    3                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   50 31
  21Q LOSS WILD-TYPE 38 23
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                81                 61 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                31                 23 
$`21Q LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR 
       25.78         7.63         5.92        13.94         8.94        32.45 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27         0.85        20.78        20.12         0.03         0.26 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A6F8 TCGA-JY-A93C TCGA-JY-A93D 
        0.53         0.79         0.13       122.10        23.18        25.28 
TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       17.59         3.16         3.45         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP 
        3.52         3.35        19.50         6.41         4.08         7.17 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        30.74         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        6.94         2.60         0.36         7.40         3.95         3.02 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NR 
        2.66        12.92        16.47        13.55        13.22         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        27.12        52.57        46.09        10.36         0.07 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A4A3 
        0.07         0.33         0.10         0.13         0.07         0.07 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.10         0.10         0.07         0.20        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
        3.78         8.02         7.59         5.06         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EW 
        6.35         9.30         4.80         8.15         4.44         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA7D TCGA-ZR-A9CJ 
       36.72         9.17        18.12 

$`21Q LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3QL 
       31.27        14.30        58.55        16.24         4.21        20.09 
TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP 
        2.63         0.99        17.03        23.41         0.36        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        0.46         0.43        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93E TCGA-KH-A6WC 
       41.52        42.77        25.41        15.48        18.08         6.21 
TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A88T 
        3.68         8.78        18.35         3.32         1.38         8.71 
TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN 
       25.12        55.50        35.97        13.48         7.76         5.42 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49U TCGA-LN-A49V 
       21.37        83.24        10.45         0.16         0.07         0.10 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10         0.07         0.13         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A5U7 TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BV 
        0.07         1.18        14.70        53.95         7.00         8.78 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-AA4G 
       14.01         5.29         3.42         8.48        18.31        12.03 
TCGA-VR-AA7I 
       15.91 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.03               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            122.10              83.24 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              7.04               8.78 
[1] "0.0 - 122.1 (7.0)" "0.1 - 83.2 (8.8)" 
[1] "hr=" "1.4"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q LOSS MUTATED         6        3        5        1        14        11
  21Q LOSS WILD-TYPE       2        1        1        0        21        15
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED          14          5          6          4        2
  21Q LOSS WILD-TYPE         9          6          2          2        1
                    vv
clus                 STAGE IVA
  21Q LOSS MUTATED           1
  21Q LOSS WILD-TYPE         1
D78V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   6                  2
  STAGE IA                  3                  1
  STAGE IB                  5                  1
  STAGE II                  1                  0
  STAGE IIA                14                 21
  STAGE IIB                11                 15
  STAGE III                14                  9
  STAGE IIIA                5                  6
  STAGE IIIB                6                  2
  STAGE IIIC                4                  2
  STAGE IV                  2                  1
  STAGE IVA                 1                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  21Q LOSS MUTATED      15 15 43  2
  21Q LOSS WILD-TYPE    11 18 31  2
D78V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1               15                 11
  T2                  15                 18
  T3                  43                 31
  T4                   2                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  21Q LOSS MUTATED   35 29  7  4
  21Q LOSS WILD-TYPE 29 25  4  2
D78V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               35                 29
  N1               29                 25
  N2                7                  4
  N3                4                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  21Q LOSS MUTATED   61  1   2  9
  21Q LOSS WILD-TYPE 50  1   1  8
D78V6, multiclass
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0                61                 50
  M1                 1                  1
  M1A                2                  1
  MX                 9                  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"
D78V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   15 70
  21Q LOSS WILD-TYPE  6 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     15   70
  21Q LOSS WILD-TYPE    6   59
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               15                  6
  MALE                 70                 59
[1] 2 2
[1] FALSE
D78V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED      18                         0    56
  21Q LOSS WILD-TYPE    20                         2    37
D78V9, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                   18                 20
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   56                 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"

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   34 27
  22Q LOSS WILD-TYPE 54 27
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                61                 81 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                27                 27 
$`22Q LOSS MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3YB TCGA-IG-A4P3 
        8.94        16.24         4.21        32.45         2.63         0.03 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-JY-A6F8 
        0.26         0.53         0.79        23.41         0.46       122.10 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OG 
       42.77        25.41        25.28         3.16         3.52         3.35 
TCGA-L5-A4OH TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88Y 
       19.50        30.74         4.90        29.00         7.13         0.36 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NW 
       16.47        13.55        13.22         5.42         8.71        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
       10.36         0.07        10.45         0.33         0.10         0.07 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.07         0.10         0.07         8.02         7.59         5.06 
TCGA-R6-A6XG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EU 
       29.59         7.00         5.29         4.80         8.15        18.31 
TCGA-ZR-A9CJ 
       18.12 

$`22Q LOSS WILD-TYPE`
TCGA-2H-A9GF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
       25.78        33.27        20.09         0.85        20.78        20.12 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
        0.99        17.03         0.36         0.13        14.86         0.43 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       44.75        60.39        68.02         3.68        41.52        15.48 
TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       23.18        18.08        17.59         6.21         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        4.31         8.94         3.68         8.78         6.41         4.08 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OX 
       18.35         3.32         7.17         1.38         3.16         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A8NG 
        6.94         8.71         2.60        25.12         3.95        35.97 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76        21.37        13.41        27.12        83.24        52.57 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A2 
        0.16         0.07         0.13         0.10         0.07         0.13 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10         0.10         0.10         0.07         0.07         0.10 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.07         0.20         1.18        17.62         5.16         3.78 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BV 
       14.70         7.04         6.35        53.95         9.30         8.78 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-A8Q7 
       14.01         3.42         8.48         4.44         8.12        36.72 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       12.03         9.17        15.91 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.03               0.07 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            122.10              83.24 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              7.63               7.17 
[1] "0.0 - 122.1 (7.6)" "0.1 - 83.2 (7.2)" 
[1] "hr=" "1.3"
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED         5        0        3        0        11        10
  22Q LOSS WILD-TYPE       3        4        3        1        24        16
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED          14          2          3          3        3
  22Q LOSS WILD-TYPE         9          9          5          3        0
                    vv
clus                 STAGE IVA
  22Q LOSS MUTATED           2
  22Q LOSS WILD-TYPE         0
D79V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   5                  3
  STAGE IA                  0                  4
  STAGE IB                  3                  3
  STAGE II                  0                  1
  STAGE IIA                11                 24
  STAGE IIB                10                 16
  STAGE III                14                  9
  STAGE IIIA                2                  9
  STAGE IIIB                3                  5
  STAGE IIIC                3                  3
  STAGE IV                  3                  0
  STAGE IVA                 2                  0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  22Q LOSS MUTATED      15 10 33  0
  22Q LOSS WILD-TYPE    11 23 41  4
D79V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1               15                 11
  T2                  10                 23
  T3                  33                 41
  T4                   0                  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                 N0 N1 N2 N3
  22Q LOSS MUTATED   22 30  3  3
  22Q LOSS WILD-TYPE 42 24  8  3
D79V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               22                 42
  N1               30                 24
  N2                3                  8
  N3                3                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  22Q LOSS MUTATED   48  2   3  4
  22Q LOSS WILD-TYPE 63  0   0 13
D79V6, multiclass
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0                48                 63
  M1                 2                  0
  M1A                3                  0
  MX                 4                 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"
D79V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   10 54
  22Q LOSS WILD-TYPE 11 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     10   54
  22Q LOSS WILD-TYPE   11   75
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               10                 11
  MALE                 54                 75
[1] 2 2
[1] FALSE
D79V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED      13                         0    38
  22Q LOSS WILD-TYPE    25                         2    55
D79V9, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                   13                 25
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   38                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   22 12
  XQ LOSS WILD-TYPE 66 42
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               34               108 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               12                42 
$`XQ LOSS MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A625 TCGA-JY-A6FA TCGA-JY-A6FH 
       25.78         4.21        32.45         0.36        44.75        42.77 
TCGA-JY-A938 TCGA-JY-A93C TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OJ TCGA-L5-A4ON 
       25.41        23.18         3.45         3.52         6.41        18.35 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NR 
        7.17         3.16         3.95        13.48        16.47         8.71 
TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-LN-A4A9 
       46.09         0.16         0.10         0.07         0.10         0.07 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-V5-A7RC 
        0.07         1.18        17.62         8.02         5.06         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8Q7 
        4.80         8.15         4.44        36.72 

$`XQ LOSS WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        8.94        16.24        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12         0.03         0.26         0.99         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        23.41         0.13        14.86         0.46 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        0.43       122.10        60.39        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       15.48        25.28        18.08        17.59         6.21         3.16 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         4.31         8.94         3.68         3.35        19.50 
TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
        8.78         4.08         3.32         1.38        30.74         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         0.36         7.40         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       35.97        12.92        13.55        13.22         7.76         5.42 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ 
       21.37        13.41        27.12        83.24        52.57        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
        0.07        10.45         0.07         0.33         0.13         0.07 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10         0.07         0.10         0.13         0.07         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.10         0.07         0.10         0.20         5.16         3.78 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV 
        9.30         7.00         8.78        14.01         5.29         8.48 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ 
       18.31         8.12        12.03         9.17        15.91        18.12 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.07              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            46.09            122.10 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            5.735             7.695 
[1] "0.1 - 46.1 (5.7)"  "0.0 - 122.1 (7.7)"
[1] "hr=" "1"  
D80V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ LOSS MUTATED         2        2        2        0        11         4
  XQ LOSS WILD-TYPE       6        2        4        1        24        22
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED           6          1          3          0        0
  XQ LOSS WILD-TYPE        17         10          5          6        3
                   vv
clus                STAGE IVA
  XQ LOSS MUTATED           0
  XQ LOSS WILD-TYPE         2
D80V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  2                 6
  STAGE IA                 2                 2
  STAGE IB                 2                 4
  STAGE II                 0                 1
  STAGE IIA               11                24
  STAGE IIB                4                22
  STAGE III                6                17
  STAGE IIIA               1                10
  STAGE IIIB               3                 5
  STAGE IIIC               0                 6
  STAGE IV                 0                 3
  STAGE IVA                0                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  XQ LOSS MUTATED       6 10 16  0
  XQ LOSS WILD-TYPE    20 23 58  4
D80V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1               6                20
  T2                 10                23
  T3                 16                58
  T4                  0                 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                N0 N1 N2 N3
  XQ LOSS MUTATED   17 12  3  0
  XQ LOSS WILD-TYPE 47 42  8  6
D80V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              17                47
  N1              12                42
  N2               3                 8
  N3               0                 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                M0 M1 M1A MX
  XQ LOSS MUTATED   28  0   0  2
  XQ LOSS WILD-TYPE 83  2   3 15
D80V6, multiclass
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0               28                83
  M1                0                 2
  M1A               0                 3
  MX                2                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    3 34
  XQ LOSS WILD-TYPE 18 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3   34
  XQ LOSS WILD-TYPE   18   95
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               3                18
  MALE                34                95
[1] 2 2
[1] FALSE
D80V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED      13                         1    18
  XQ LOSS WILD-TYPE    25                         1    75
D80V9, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                  13                25
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  18                75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
