[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/10005875/ESCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/10013680/transformed.cor.cli.txt"

nPatients in clinical file=127, in cluster file=126, common to both=105
[1]  80 105
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               17                88 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               17                88 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32                73 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32                73 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               38                67 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               38                67 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               27                78 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               27                78 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               13                92 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               13                92 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               41                64 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               41                64 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8                97 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8                97 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6                99 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6                99 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               42                63 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               42                63 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               16                89 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               16                89 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               21                84 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               21                84 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               17                88 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               17                88 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               62                43 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               62                43 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               48                57 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               48                57 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               40                65 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               40                65 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               56                49 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               56                49 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                8                97 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                8                97 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               19                86 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               19                86 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                20                 85 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                20                 85 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                14                 91 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                14                 91 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                19                 86 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                19                 86 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                20                 85 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                20                 85 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                36                 69 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                36                 69 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                21                 84 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                21                 84 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                25                 80 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                25                 80 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                27                 78 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                27                 78 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                20                 85 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                20                 85 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                22                 83 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                22                 83 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                18                 87 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                18                 87 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                18                 87 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                18                 87 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                24                 81 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                24                 81 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                29                 76 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                29                 76 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                15                 90 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                15                 90 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                13                 92 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                13                 92 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                19                 86 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                19                 86 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                54                 51 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                54                 51 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                61                 44 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                61                 44 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 8                 97 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 8                 97 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                19                 86 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                19                 86 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               22                83 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               22                83 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               22                83 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               22                83 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               14                91 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               14                91 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5               100 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5               100 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               13                92 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               13                92 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               54                51 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               54                51 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               14                91 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               14                91 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               59                46 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               59                46 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               55                50 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               55                50 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               28                77 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               28                77 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               44                61 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               44                61 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               21                84 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               21                84 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               21                84 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               21                84 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                8                97 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                8                97 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               11                94 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               11                94 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               32                73 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               32                73 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               10                95 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               10                95 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               57                48 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               57                48 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               36                69 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               36                69 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                24                 81 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                24                 81 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                29                 76 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                29                 76 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                31                 74 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                31                 74 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                32                 73 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                32                 73 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                19                 86 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                19                 86 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                15                 90 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                15                 90 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                40                 65 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                40                 65 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                27                 78 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                27                 78 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                26                 79 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                26                 79 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                30                 75 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                30                 75 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                30                 75 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                30                 75 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                39                 66 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                39                 66 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                 93 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                 93 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                37                 68 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                37                 68 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                53                 52 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                53                 52 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                34                 71 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                34                 71 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                26                 79 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                26                 79 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                15                 90 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                15                 90 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                 99 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                 99 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                61                 44 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                61                 44 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                39                 66 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                39                 66 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               24                81 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               24                81 
[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 105 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        1012          611           NA          632           80          612 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
           1            8           30           16          518           NA 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA 
          11            4           34           14         3714           NA 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC 
        1837         1638           NA           NA         1301          189 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
          96          105           NA           NA          272          107 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
         112          102          593          267          195          124 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
          NA          101          218           NA           NA          935 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
          NA          882           NA           NA          211          265 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
          79           NA           11          225          120           92 
TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
         501           NA           NA          315            2          318 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
           5            2           10           NA            3            4 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
           2            3            2            3            2           NA 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
           4            2            3            3            3            2 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
           2            3            2            6           36           NA 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU 
          NA           NA           NA           NA          536           NA 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
         115           NA           NA           NA          447           NA 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
         900           NA         1641           NA           NA          267 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
         426           NA          146 
Variable 1:'AGE':	nDistinctValues=42,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=11,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	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=32,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=8,	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 105 columns, 1 survival variables, and 8 non-survival variables.
AGE, nv=42, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=11, 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 18 26 47  3 
[1] "table(vv)"
vv
T0+T1    T2 T3+T4 
   19    26    50 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T0 T1 T2 T3 T4 
 1 18 26 47  3 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1    T2 T3+T4 
   19    26    50 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
50 33  8  3 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
   50    33    11 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 N3 
50 33  8  3 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
   50    33    11 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=32, binary=FALSE, numeric=TRUE
RACE, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED   13  4
  1P GAIN WILD-TYPE 54 27
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               17                81 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                27 
$`1P GAIN MUTATED`
TCGA-IG-A3QL TCGA-IG-A51D TCGA-IG-A8O2 TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OX 
       20.09        17.03         0.46         4.08        18.35         7.43 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        0.36         3.95         3.02        10.36         0.07        10.45 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4MR TCGA-R6-A6L4 TCGA-R6-A6XG 
        0.10         0.13         0.07        14.70        29.59 

$`1P GAIN WILD-TYPE`
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-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        0.26         0.99         0.53         0.79         0.36         0.13 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        1.12       122.10        44.75        60.39        53.85         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       41.52        42.77         6.21         3.16         3.45         0.30 
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-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-A88Z TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU 
        2.60        25.12         7.40        16.47        21.37        83.24 
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-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10         0.07         0.07         0.07         0.10         0.10 
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-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-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-A7RE 
       14.01         5.29         4.80 

  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 
             4.08              4.31 
[1] "0.1 - 29.6 (4.1)"  "0.0 - 122.1 (4.3)"
[1] "hr=" "1.3"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED         1        1        0        0         5         4
  1P GAIN WILD-TYPE       6        3        4        1        25        12
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED           0          0          1          1        0
  1P GAIN WILD-TYPE        11          8          5          2        1
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  1                 6
  STAGE IA                 1                 3
  STAGE IB                 0                 4
  STAGE II                 0                 1
  STAGE IIA                5                25
  STAGE IIB                4                12
  STAGE III                0                11
  STAGE IIIA               0                 8
  STAGE IIIB               1                 5
  STAGE IIIC               1                 2
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  1P GAIN MUTATED       5  3     7
  1P GAIN WILD-TYPE    14 23    43
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1               5                14
  T2                  3                23
  T3+T4               7                43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  1P GAIN MUTATED    9  4     2
  1P GAIN WILD-TYPE 41 29     9
D1V5, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0                  9                41
  N1                  4                29
  N2+N3               2                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  1P GAIN MUTATED   11   0  2
  1P GAIN WILD-TYPE 64   1 13
D1V6, multiclass
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               11                64
  M1A               0                 1
  MX                2                13
[1] 3 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    2 15
  1P GAIN WILD-TYPE 13 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2   15
  1P GAIN WILD-TYPE   13   75
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               2                13
  MALE                15                75
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    6 11
  1P GAIN WILD-TYPE 29 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      6   11
  1P GAIN WILD-TYPE   29   55
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN               6                29
  WHITE              11                55
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   21  9
  1Q GAIN WILD-TYPE 46 22
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               30                68 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                9                22 
$`1Q GAIN MUTATED`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A51D TCGA-IG-A5B8 
       20.09         0.85        20.12         0.03        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A8O2 TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
        0.36         0.46         0.30         3.68        19.50         4.08 
TCGA-L5-A4ON TCGA-L5-A4OX TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       18.35         7.43         0.36         7.40         3.95         3.02 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       10.36         0.07        10.45         0.07         0.10         0.10 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4MR TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-S8-A6BW 
        0.13         0.07         0.07        14.70        29.59        14.01 

$`1Q GAIN WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       33.27        20.78         2.63         0.26         0.99         0.53 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.13         1.12       122.10        44.75        60.39        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
        3.68        41.52        42.77         6.21         3.16         3.45 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ 
        4.31         8.94         3.52         3.35         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-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       16.47        21.37        83.24         0.16         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10         0.13         0.07         0.07         0.10         0.10 
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-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-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-A7RE 
        5.29         4.80 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.03              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            29.59            122.10 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             3.35              4.98 
[1] "0.0 - 29.6 (3.4)"  "0.1 - 122.1 (5.0)"
[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        2        0        10         6
  1Q GAIN WILD-TYPE       5        3        2        1        20        10
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           2          2          2          1        0
  1Q GAIN WILD-TYPE         9          6          4          2        1
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  2                 5
  STAGE IA                 1                 3
  STAGE IB                 2                 2
  STAGE II                 0                 1
  STAGE IIA               10                20
  STAGE IIB                6                10
  STAGE III                2                 9
  STAGE IIIA               2                 6
  STAGE IIIB               2                 4
  STAGE IIIC               1                 2
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  1Q GAIN MUTATED       8  7    15
  1Q GAIN WILD-TYPE    11 19    35
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1               8                11
  T2                  7                19
  T3+T4              15                35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  1Q GAIN MUTATED   17 10     3
  1Q GAIN WILD-TYPE 33 23     8
D2V5, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0                 17                33
  N1                 10                23
  N2+N3               3                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  1Q GAIN MUTATED   24   0  3
  1Q GAIN WILD-TYPE 51   1 12
D2V6, multiclass
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0               24                51
  M1A               0                 1
  MX                3                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    3 29
  1Q GAIN WILD-TYPE 12 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3   29
  1Q GAIN WILD-TYPE   12   61
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               3                12
  MALE                29                61
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   12 20
  1Q GAIN WILD-TYPE 23 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     12   20
  1Q GAIN WILD-TYPE   23   46
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN              12                23
  WHITE              20                46
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED   23 13
  2P GAIN WILD-TYPE 44 18
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               36                62 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               13                18 
$`2P GAIN MUTATED`
TCGA-IG-A4P3 TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OH 
        0.03         0.46        44.75         4.31         3.68        19.50 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88V 
        4.08        18.35         3.32         3.16         7.13         2.60 
TCGA-L5-A88Y TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49S 
        0.36        10.36         0.07        10.45         0.10         0.13 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ 
        0.07         0.13         0.07         0.10         0.10         0.10 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.20         1.18         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-A7RE 
        7.04        29.59         6.35        53.95        14.01         4.80 

$`2P GAIN WILD-TYPE`
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-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
        0.26         0.99         0.53        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        0.13         1.12       122.10        60.39        53.85         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       41.52        42.77         6.21         3.16         3.45         0.30 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OP 
        8.94         3.52         3.35         8.78         6.41         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        1.38        30.74         4.90        29.00         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ 
        8.71        25.12         7.40         3.95         3.02        16.47 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U 
       21.37        83.24         0.16         0.07         0.33         0.07 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.10         0.07         0.10         0.10         0.07         0.07 
TCGA-LN-A4MR TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6Y2 TCGA-RE-A7BO 
        0.07        17.62         5.16         3.78         9.30         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB 
        8.78         5.29 

  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 
             3.88              5.03 
[1] "0.0 - 54.0 (3.9)"  "0.1 - 122.1 (5.0)"
[1] "hr=" "1.6"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         1        2        2        1         8         7
  2P GAIN WILD-TYPE       6        2        2        0        22         9
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED           5          0          1          2        0
  2P GAIN WILD-TYPE         6          8          5          1        1
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  1                 6
  STAGE IA                 2                 2
  STAGE IB                 2                 2
  STAGE II                 1                 0
  STAGE IIA                8                22
  STAGE IIB                7                 9
  STAGE III                5                 6
  STAGE IIIA               0                 8
  STAGE IIIB               1                 5
  STAGE IIIC               2                 1
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  2P GAIN MUTATED       7  9    14
  2P GAIN WILD-TYPE    12 17    36
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1               7                12
  T2                  9                17
  T3+T4              14                36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  2P GAIN MUTATED   16 11     3
  2P GAIN WILD-TYPE 34 22     8
D3V5, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0                 16                34
  N1                 11                22
  N2+N3               3                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  2P GAIN MUTATED   21   0  6
  2P GAIN WILD-TYPE 54   1  9
D3V6, multiclass
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0               21                54
  M1A               0                 1
  MX                6                 9
[1] 3 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    3 35
  2P GAIN WILD-TYPE 12 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3   35
  2P GAIN WILD-TYPE   12   55
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               3                12
  MALE                35                55
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   16 21
  2P GAIN WILD-TYPE 19 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     16   21
  2P GAIN WILD-TYPE   19   45
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN              16                19
  WHITE              21                45
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED   17  8
  2Q GAIN WILD-TYPE 50 23
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               25                73 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                8                23 
$`2Q GAIN MUTATED`
TCGA-JY-A6FA TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OW 
       44.75         4.31         3.68        19.50         3.32         7.13 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A4A2 TCGA-LN-A4A4 
        2.60         0.36         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-S8-A6BW 
        5.06        14.70        29.59         6.35        53.95        14.01 
TCGA-V5-A7RE 
        4.80 

$`2Q GAIN WILD-TYPE`
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-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-JY-A6F8 TCGA-JY-A6FB 
        0.36         0.13         1.12         0.46       122.10        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C 
       53.85         3.68        41.52        42.77         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI 
        3.45         0.30         8.94         3.52         3.35         8.78 
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-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-A893 TCGA-L5-A8NJ TCGA-L5-A8NQ 
       25.12         7.40         3.95         3.02        16.47        21.37 
TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       83.24        10.36        10.45         0.16         0.07         0.33 
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-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-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
       17.62         5.16         7.04         9.30         7.00         8.78 
TCGA-V5-A7RB 
        5.29 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.07              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            53.95            122.10 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             4.31              4.08 
[1] "0.1 - 54.0 (4.3)"  "0.0 - 122.1 (4.1)"
[1] "hr=" "1.1"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q GAIN MUTATED         1        0        2        1         5         5
  2Q GAIN WILD-TYPE       6        4        2        0        25        11
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           3          0          1          1        0
  2Q GAIN WILD-TYPE         8          8          5          2        1
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  1                 6
  STAGE IA                 0                 4
  STAGE IB                 2                 2
  STAGE II                 1                 0
  STAGE IIA                5                25
  STAGE IIB                5                11
  STAGE III                3                 8
  STAGE IIIA               0                 8
  STAGE IIIB               1                 5
  STAGE IIIC               1                 2
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  2Q GAIN MUTATED       4  7     9
  2Q GAIN WILD-TYPE    15 19    41
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1               4                15
  T2                  7                19
  T3+T4               9                41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  2Q GAIN MUTATED   11  7     2
  2Q GAIN WILD-TYPE 39 26     9
D4V5, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0                 11                39
  N1                  7                26
  N2+N3               2                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  2Q GAIN MUTATED   15   0  4
  2Q GAIN WILD-TYPE 60   1 11
D4V6, multiclass
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0               15                60
  M1A               0                 1
  MX                4                11
[1] 3 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    2 25
  2Q GAIN WILD-TYPE 13 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   25
  2Q GAIN WILD-TYPE   13   65
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               2                13
  MALE                25                65
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   10 16
  2Q GAIN WILD-TYPE 25 50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     10   16
  2Q GAIN WILD-TYPE   25   50
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN              10                25
  WHITE              16                50
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    4  8
  3P GAIN WILD-TYPE 63 23
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               12                86 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                8                23 
$`3P GAIN MUTATED`
TCGA-IG-A4P3 TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A891 
        0.03         0.30         4.31         4.08         3.16         3.95 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6XQ 
       10.36        10.45         0.10         5.16         5.06         6.35 

$`3P GAIN WILD-TYPE`
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-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
        0.26         0.99         0.53        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
        0.13         1.12         0.46       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C 
       53.85         3.68        41.52        42.77         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        3.45         8.94         3.52         3.68         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-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-A893 
        8.71         2.60        25.12         0.36         7.40         3.02 
TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       16.47        21.37        83.24         0.07         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.33         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-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       17.62         3.78         8.02         7.59        14.70         7.04 
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-A7RE 
        5.29         4.80 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.03              0.07 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            10.45            122.10 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            4.195             4.290 
[1] "0.0 - 10.4 (4.2)"  "0.1 - 122.1 (4.3)"
[1] "hr=" "4.4"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED         0        2        0        0         2         2
  3P GAIN WILD-TYPE       7        2        4        1        28        14
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED           2          0          1          1        0
  3P GAIN WILD-TYPE         9          8          5          2        1
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  0                 7
  STAGE IA                 2                 2
  STAGE IB                 0                 4
  STAGE II                 0                 1
  STAGE IIA                2                28
  STAGE IIB                2                14
  STAGE III                2                 9
  STAGE IIIA               0                 8
  STAGE IIIB               1                 5
  STAGE IIIC               1                 2
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  3P GAIN MUTATED       2  2     7
  3P GAIN WILD-TYPE    17 24    43
D5V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1               2                17
  T2                  2                24
  T3+T4               7                43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  3P GAIN MUTATED    5  4     2
  3P GAIN WILD-TYPE 45 29     9
D5V5, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0                  5                45
  N1                  4                29
  N2+N3               2                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  3P GAIN MUTATED    7   0  3
  3P GAIN WILD-TYPE 68   1 12
D5V6, multiclass
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0                7                68
  M1A               0                 1
  MX                3                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    2 11
  3P GAIN WILD-TYPE 13 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   11
  3P GAIN WILD-TYPE   13   79
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               2                13
  MALE                11                79
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    3 10
  3P GAIN WILD-TYPE 32 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3   10
  3P GAIN WILD-TYPE   32   56
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN               3                32
  WHITE              10                56
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED   26 13
  3Q GAIN WILD-TYPE 41 18
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               39                59 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               13                18 
$`3Q GAIN MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27        20.09         0.85         2.63         0.03         0.26 
TCGA-IG-A50L TCGA-IG-A51D TCGA-JY-A6FB TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM 
        0.53        17.03        60.39         0.30         4.31         4.08 
TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NJ 
        3.16         7.13         6.94         2.60         3.95        16.47 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.36        10.45         0.07         0.33         0.10         0.13 
TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10         0.13         0.07         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.07         0.10         5.16         8.02         7.59         5.06 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-S8-A6BW 
        6.35        53.95        14.01 

$`3Q GAIN WILD-TYPE`
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
       20.78        20.12         0.99         0.79         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        1.12         0.46       122.10        44.75        53.85         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M 
       41.52        42.77         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-A8NQ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49U 
        3.02        21.37        83.24         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-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        9.30         7.00         8.78         5.29         4.80 

  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 
             3.16              5.29 
[1] "0.0 - 60.4 (3.2)"  "0.1 - 122.1 (5.3)"
[1] "hr=" "1.6"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED         1        2        2        0        11         6
  3Q GAIN WILD-TYPE       6        2        2        1        19        10
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED           7          3          2          1        0
  3Q GAIN WILD-TYPE         4          5          4          2        1
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  1                 6
  STAGE IA                 2                 2
  STAGE IB                 2                 2
  STAGE II                 0                 1
  STAGE IIA               11                19
  STAGE IIB                6                10
  STAGE III                7                 4
  STAGE IIIA               3                 5
  STAGE IIIB               2                 4
  STAGE IIIC               1                 2
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  3Q GAIN MUTATED       4  9    23
  3Q GAIN WILD-TYPE    15 17    27
D6V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1               4                15
  T2                  9                17
  T3+T4              23                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  3Q GAIN MUTATED   19 14     3
  3Q GAIN WILD-TYPE 31 19     8
D6V5, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0                 19                31
  N1                 14                19
  N2+N3               3                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  3Q GAIN MUTATED   29   0  6
  3Q GAIN WILD-TYPE 46   1  9
D6V6, multiclass
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0               29                46
  M1A               0                 1
  MX                6                 9
[1] 3 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    5 36
  3Q GAIN WILD-TYPE 10 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5   36
  3Q GAIN WILD-TYPE   10   54
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               5                10
  MALE                36                54
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   16 24
  3Q GAIN WILD-TYPE 19 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     16   24
  3Q GAIN WILD-TYPE   19   42
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN              16                19
  WHITE              24                42
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED    5  2
  4P GAIN WILD-TYPE 62 29
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                7                91 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                29 
$`4P GAIN MUTATED`
TCGA-IG-A3YB TCGA-JY-A6F8 TCGA-L5-A43J TCGA-L5-A4ON TCGA-LN-A4A9 TCGA-R6-A6XG 
        2.63       122.10         4.31        18.35         0.07        29.59 
TCGA-R6-A6Y0 
       53.95 

$`4P GAIN WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09         0.85        20.78        20.12         0.03 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
        0.26         0.99         0.53        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.13         1.12         0.46        44.75        60.39        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
        3.68        41.52        42.77         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-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ 
        3.95         3.02        16.47        21.37        83.24        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-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 
        4.80 

  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 
            18.35              3.95 
[1] "0.1 - 122.1 (18.4)" "0.0 - 83.2 (4.0)"  
[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         1         2
  4P GAIN WILD-TYPE       6        4        4        1        29        14
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED           1          1          0          0        0
  4P GAIN WILD-TYPE        10          7          6          3        1
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  1                 6
  STAGE IA                 0                 4
  STAGE IB                 0                 4
  STAGE II                 0                 1
  STAGE IIA                1                29
  STAGE IIB                2                14
  STAGE III                1                10
  STAGE IIIA               1                 7
  STAGE IIIB               0                 6
  STAGE IIIC               0                 3
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  4P GAIN MUTATED       2  1     3
  4P GAIN WILD-TYPE    17 25    47
D7V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1               2                17
  T2                  1                25
  T3+T4               3                47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  4P GAIN MUTATED    3  3     0
  4P GAIN WILD-TYPE 47 30    11
D7V5, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0                  3                47
  N1                  3                30
  N2+N3               0                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  4P GAIN MUTATED    4   0  1
  4P GAIN WILD-TYPE 71   1 14
D7V6, multiclass
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0                4                71
  M1A               0                 1
  MX                1                14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    0  8
  4P GAIN WILD-TYPE 15 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    8
  4P GAIN WILD-TYPE   15   82
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               0                15
  MALE                 8                82
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    2  6
  4P GAIN WILD-TYPE 33 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    6
  4P GAIN WILD-TYPE   33   60
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN               2                33
  WHITE               6                60
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED    3  2
  4Q GAIN WILD-TYPE 64 29
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5                93 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                29 
$`4Q GAIN MUTATED`
TCGA-JY-A6F8 TCGA-L5-A43H TCGA-L5-A4ON TCGA-LN-A4A9 TCGA-R6-A6Y0 
      122.10         0.30        18.35         0.07        53.95 

$`4Q GAIN WILD-TYPE`
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-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-JY-A6FA TCGA-JY-A6FB 
        0.36         0.13         1.12         0.46        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C 
       53.85         3.68        41.52        42.77         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.45         4.31         8.94         3.52         3.68         3.35 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
       19.50         8.78         6.41         4.08         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-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU 
        7.40         3.95         3.02        16.47        21.37        83.24 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         0.07        10.45         0.16         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-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-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
        7.04        29.59         6.35         9.30         7.00         8.78 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
       14.01         5.29         4.80 

  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 
            18.35              4.08 
[1] "0.1 - 122.1 (18.4)" "0.0 - 83.2 (4.1)"  
[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         1         1
  4Q GAIN WILD-TYPE       6        4        4        1        29        15
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED           2          0          0          0        0
  4Q GAIN WILD-TYPE         9          8          6          3        1
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  1                 6
  STAGE IA                 0                 4
  STAGE IB                 0                 4
  STAGE II                 0                 1
  STAGE IIA                1                29
  STAGE IIB                1                15
  STAGE III                2                 9
  STAGE IIIA               0                 8
  STAGE IIIB               0                 6
  STAGE IIIC               0                 3
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  4Q GAIN MUTATED       2  1     2
  4Q GAIN WILD-TYPE    17 25    48
D8V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1               2                17
  T2                  1                25
  T3+T4               2                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  4Q GAIN MUTATED    2  3     0
  4Q GAIN WILD-TYPE 48 30    11
D8V5, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0                  2                48
  N1                  3                30
  N2+N3               0                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  4Q GAIN MUTATED    4   0  0
  4Q GAIN WILD-TYPE 71   1 15
D8V6, multiclass
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0                4                71
  M1A               0                 1
  MX                0                15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    0  6
  4Q GAIN WILD-TYPE 15 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    6
  4Q GAIN WILD-TYPE   15   84
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               0                15
  MALE                 6                84
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    2  4
  4Q GAIN WILD-TYPE 33 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    4
  4Q GAIN WILD-TYPE   33   62
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN               2                33
  WHITE               4                62
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   27 11
  5P GAIN WILD-TYPE 40 20
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               38                60 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11                20 
$`5P GAIN MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-JY-A6FA 
       33.27         2.63        20.12         0.03         0.79        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       53.85         3.68        42.77         0.30         4.31         8.94 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR 
       19.50         8.78         4.08         3.32         7.17         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88Y TCGA-L7-A6VZ 
        4.90        29.00         7.13         6.94         0.36        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-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6Y0 
        0.10         0.07         0.20         5.06        14.70        53.95 
TCGA-RE-A7BO TCGA-S8-A6BW 
        7.00        14.01 

$`5P GAIN WILD-TYPE`
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-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 
       17.03         0.36         0.13         1.12         0.46       122.10 
TCGA-JY-A6FB TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OE 
       60.39        41.52         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-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49L 
        3.02        16.47        21.37        83.24         0.07        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
        0.16         0.07         0.13         0.07         0.10         0.10 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 
        0.13         0.07         0.10         0.07         0.07         1.18 
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-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
       29.59         6.35         9.30         8.78         5.29         4.80 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.03              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            53.95            122.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            4.605             3.865 
[1] "0.0 - 54.0 (4.6)"  "0.1 - 122.1 (3.9)"
[1] "hr=" "1.2"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED         1        3        3        1        10         7
  5P GAIN WILD-TYPE       6        1        1        0        20         9
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED           6          2          0          3        1
  5P GAIN WILD-TYPE         5          6          6          0        0
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  1                 6
  STAGE IA                 3                 1
  STAGE IB                 3                 1
  STAGE II                 1                 0
  STAGE IIA               10                20
  STAGE IIB                7                 9
  STAGE III                6                 5
  STAGE IIIA               2                 6
  STAGE IIIB               0                 6
  STAGE IIIC               3                 0
  STAGE IV                 1                 0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  5P GAIN MUTATED       6 11    22
  5P GAIN WILD-TYPE    13 15    28
D9V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1               6                13
  T2                 11                15
  T3+T4              22                28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  5P GAIN MUTATED   20 15     4
  5P GAIN WILD-TYPE 30 18     7
D9V5, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0                 20                30
  N1                 15                18
  N2+N3               4                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  5P GAIN MUTATED   28   1  9
  5P GAIN WILD-TYPE 47   0  6
D9V6, multiclass
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0               28                47
  M1A               1                 0
  MX                9                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    7 35
  5P GAIN WILD-TYPE  8 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7   35
  5P GAIN WILD-TYPE    8   55
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               7                 8
  MALE                35                55
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   15 25
  5P GAIN WILD-TYPE 20 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     15   25
  5P GAIN WILD-TYPE   20   41
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN              15                20
  WHITE              25                41
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED   10  3
  5Q GAIN WILD-TYPE 57 28
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               13                85 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                28 
$`5Q GAIN MUTATED`
TCGA-IG-A3I8 TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OO 
       33.27         0.30         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 
        7.00 

$`5Q GAIN WILD-TYPE`
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-A625 
        0.26         0.99         0.53        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
        0.13         1.12         0.46       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C 
       53.85         3.68        41.52        42.77         6.21         3.16 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ 
        3.45         4.31         3.52         3.68         3.35         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-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.13         7.43         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ 
       25.12         0.36         7.40         3.95         3.02        16.47 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       21.37        83.24         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-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.10         0.13         0.07         0.10         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 
        0.07         0.07         0.10         0.20         1.18        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG 
        5.16         3.78         8.02         7.59         7.04        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 
        4.80 

  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 
             7.00              3.78 
[1] "0.1 - 33.3 (7.0)"  "0.0 - 122.1 (3.8)"
[1] "hr=" "1.5"
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       6        4        3        1        24        15
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED           1          0          0          3        0
  5Q GAIN WILD-TYPE        10          8          6          0        1
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  1                 6
  STAGE IA                 0                 4
  STAGE IB                 1                 3
  STAGE II                 0                 1
  STAGE IIA                6                24
  STAGE IIB                1                15
  STAGE III                1                10
  STAGE IIIA               0                 8
  STAGE IIIB               0                 6
  STAGE IIIC               3                 0
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  5Q GAIN MUTATED       2  3     9
  5Q GAIN WILD-TYPE    17 23    41
D10V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1               2                17
  T2                  3                23
  T3+T4               9                41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  5Q GAIN MUTATED    8  2     4
  5Q GAIN WILD-TYPE 42 31     7
D10V5, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0                  8                42
  N1                  2                31
  N2+N3               4                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  5Q GAIN MUTATED   10   0  4
  5Q GAIN WILD-TYPE 65   1 11
D10V6, multiclass
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               10                65
  M1A               0                 1
  MX                4                11
[1] 3 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 13
  5Q GAIN WILD-TYPE 12 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3   13
  5Q GAIN WILD-TYPE   12   77
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               3                12
  MALE                13                77
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    5 10
  5Q GAIN WILD-TYPE 30 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      5   10
  5Q GAIN WILD-TYPE   30   56
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN               5                30
  WHITE              10                56
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   15  4
  6P GAIN WILD-TYPE 52 27
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               19                79 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4                27 
$`6P GAIN MUTATED`
TCGA-IG-A4QS TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A4OM 
        0.26         0.46       122.10        53.85         3.45         4.08 
TCGA-L5-A4OS TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NQ 
       30.74         6.94         2.60         3.95         3.02        21.37 
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 
        7.04 

$`6P GAIN WILD-TYPE`
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-A625 
        0.03         0.99         0.53        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG 
        0.13         1.12        44.75        60.39         3.68        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       42.77         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-A8NJ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
        7.40        16.47        83.24         0.07         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y 
        0.33         0.10         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-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.07         0.07         0.20         1.18        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ 
        3.78         8.02         7.59         5.06        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-A7RE 
        4.80 

  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 
             4.08              4.31 
[1] "0.1 - 122.1 (4.1)" "0.0 - 83.2 (4.3)" 
[1] "hr=" "2"  
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED         3        1        1        0         7         1
  6P GAIN WILD-TYPE       4        3        3        1        23        15
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           2          0          2          1        0
  6P GAIN WILD-TYPE         9          8          4          2        1
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  3                 4
  STAGE IA                 1                 3
  STAGE IB                 1                 3
  STAGE II                 0                 1
  STAGE IIA                7                23
  STAGE IIB                1                15
  STAGE III                2                 9
  STAGE IIIA               0                 8
  STAGE IIIB               2                 4
  STAGE IIIC               1                 2
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  6P GAIN MUTATED       4  5    10
  6P GAIN WILD-TYPE    15 21    40
D11V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1               4                15
  T2                  5                21
  T3+T4              10                40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  6P GAIN MUTATED   12  4     3
  6P GAIN WILD-TYPE 38 29     8
D11V5, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0                 12                38
  N1                  4                29
  N2+N3               3                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  6P GAIN MUTATED   15   0  3
  6P GAIN WILD-TYPE 60   1 12
D11V6, multiclass
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0               15                60
  M1A               0                 1
  MX                3                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    4 17
  6P GAIN WILD-TYPE 11 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4   17
  6P GAIN WILD-TYPE   11   73
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               4                11
  MALE                17                73
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    8 13
  6P GAIN WILD-TYPE 27 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      8   13
  6P GAIN WILD-TYPE   27   53
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN               8                27
  WHITE              13                53
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED   12  4
  6Q GAIN WILD-TYPE 55 27
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16                82 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                27 
$`6Q GAIN MUTATED`
TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A88S 
        0.26       122.10        60.39        53.85         3.45         6.94 
TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49S 
        2.60         3.02        21.37        10.36        10.45         0.13 
TCGA-LN-A49X TCGA-LN-A4MQ TCGA-R6-A6L4 TCGA-R6-A6L6 
        0.10         0.10        14.70         7.04 

$`6Q GAIN WILD-TYPE`
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-A625 
        0.03         0.99         0.53        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG 
        0.13         1.12         0.46        44.75         3.68        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       42.77         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-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-A88T 
       30.74         4.90        29.00         7.13         7.43         8.71 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NU 
       25.12         0.36         7.40         3.95        16.47        83.24 
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-A7RE 
        8.78        14.01         5.29         4.80 

  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 
            6.990             4.015 
[1] "0.1 - 122.1 (7.0)" "0.0 - 83.2 (4.0)" 
[1] "hr=" "2"  
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED         4        0        1        0         6         0
  6Q GAIN WILD-TYPE       3        4        3        1        24        16
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED           2          0          1          1        0
  6Q GAIN WILD-TYPE         9          8          5          2        1
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  4                 3
  STAGE IA                 0                 4
  STAGE IB                 1                 3
  STAGE II                 0                 1
  STAGE IIA                6                24
  STAGE IIB                0                16
  STAGE III                2                 9
  STAGE IIIA               0                 8
  STAGE IIIB               1                 5
  STAGE IIIC               1                 2
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  6Q GAIN MUTATED       4  3     8
  6Q GAIN WILD-TYPE    15 23    42
D12V4, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1               4                15
  T2                  3                23
  T3+T4               8                42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  6Q GAIN MUTATED   11  2     2
  6Q GAIN WILD-TYPE 39 31     9
D12V5, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0                 11                39
  N1                  2                31
  N2+N3               2                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  6Q GAIN MUTATED   12   0  3
  6Q GAIN WILD-TYPE 63   1 12
D12V6, multiclass
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0               12                63
  M1A               0                 1
  MX                3                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    2 15
  6Q GAIN WILD-TYPE 13 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2   15
  6Q GAIN WILD-TYPE   13   75
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               2                13
  MALE                15                75
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    6 11
  6Q GAIN WILD-TYPE 29 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      6   11
  6Q GAIN WILD-TYPE   29   55
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN               6                29
  WHITE              11                55
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   42 18
  7P GAIN WILD-TYPE 25 13
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               60                38 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               18                13 
$`7P GAIN MUTATED`
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-JY-A6FB TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
        0.79        60.39         3.16         3.45         0.30         4.31 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO 
        3.52         3.68         3.35        19.50        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88S 
        1.38         3.16        30.74         4.90         7.13         6.94 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L7-A6VZ 
        2.60         0.36         3.95         3.02        16.47        10.36 
TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V 
        0.07         0.07         0.33         0.10         0.07         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
        0.07         0.10         0.13         0.07         0.10         0.10 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FW 
        0.07         0.10         0.07         0.20         1.18         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 

$`7P GAIN WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A625 
       33.27         0.85        20.78         0.26         0.99         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        0.13         1.12         0.46       122.10        44.75        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OI 
        3.68        41.52        42.77         6.21         8.94         8.78 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T 
        6.41         4.08         7.17        29.00         7.43         8.71 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M 
       25.12         7.40        21.37        83.24        10.45         0.16 
TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.13         0.07         0.10         0.07        17.62         5.16 
TCGA-S8-A6BV TCGA-V5-A7RE 
        8.78         4.80 

  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 
            3.400             7.285 
[1] "0.0 - 60.4 (3.4)"  "0.1 - 122.1 (7.3)"
[1] "hr=" "1.6"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED         5        1        3        1        11        11
  7P GAIN WILD-TYPE       2        3        1        0        19         5
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED           8          4          2          2        1
  7P GAIN WILD-TYPE         3          4          4          1        0
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  5                 2
  STAGE IA                 1                 3
  STAGE IB                 3                 1
  STAGE II                 1                 0
  STAGE IIA               11                19
  STAGE IIB               11                 5
  STAGE III                8                 3
  STAGE IIIA               4                 4
  STAGE IIIB               2                 4
  STAGE IIIC               2                 1
  STAGE IV                 1                 0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  7P GAIN MUTATED      12 12    28
  7P GAIN WILD-TYPE     7 14    22
D13V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1              12                 7
  T2                 12                14
  T3+T4              28                22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  7P GAIN MUTATED   24 23     5
  7P GAIN WILD-TYPE 26 10     6
D13V5, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0                 24                26
  N1                 23                10
  N2+N3               5                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  7P GAIN MUTATED   39   1  9
  7P GAIN WILD-TYPE 36   0  6
D13V6, multiclass
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0               39                36
  M1A               1                 0
  MX                9                 6
[1] 3 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    6 56
  7P GAIN WILD-TYPE  9 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      6   56
  7P GAIN WILD-TYPE    9   34
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               6                 9
  MALE                56                34
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   20 40
  7P GAIN WILD-TYPE 15 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     20   40
  7P GAIN WILD-TYPE   15   26
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN              20                15
  WHITE              40                26
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   34 12
  7Q GAIN WILD-TYPE 33 19
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               46                52 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               12                19 
$`7Q GAIN MUTATED`
TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A51D TCGA-JY-A6FB TCGA-L5-A43C 
       20.09        20.12         0.03        17.03        60.39         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-A4OM TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A88S 
       19.50         4.08         3.32         3.16         4.90         6.94 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L7-A6VZ TCGA-LN-A49K 
        2.60         0.36         3.95         3.02        10.36         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A6 
        0.33         0.10         0.07         0.10         0.13         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 
        9.30         7.00        14.01         5.29 

$`7Q GAIN WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT 
       33.27         0.85        20.78         2.63         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.53         0.79         0.36         0.13         1.12         0.46 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        53.85         3.68        41.52        42.77 
TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP 
        6.21         8.94         8.78         6.41        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
        1.38        30.74        29.00         7.13         7.43         8.71 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L 
       25.12         7.40        16.47        21.37        83.24        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.16         0.07         0.13         0.07         0.10         0.07 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DQ 
        0.07         0.10         0.10        17.62         5.16         7.59 
TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-S8-A6BV TCGA-V5-A7RE 
        5.06        53.95         8.78         4.80 

  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 
            3.485             6.770 
[1] "0.0 - 60.4 (3.5)"  "0.1 - 122.1 (6.8)"
[1] "hr=" "1.2"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED         5        2        2        1        11         7
  7Q GAIN WILD-TYPE       2        2        2        0        19         9
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED           4          1          2          2        1
  7Q GAIN WILD-TYPE         7          7          4          1        0
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  5                 2
  STAGE IA                 2                 2
  STAGE IB                 2                 2
  STAGE II                 1                 0
  STAGE IIA               11                19
  STAGE IIB                7                 9
  STAGE III                4                 7
  STAGE IIIA               1                 7
  STAGE IIIB               2                 4
  STAGE IIIC               2                 1
  STAGE IV                 1                 0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  7Q GAIN MUTATED      12  9    20
  7Q GAIN WILD-TYPE     7 17    30
D14V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1              12                 7
  T2                  9                17
  T3+T4              20                30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  7Q GAIN MUTATED   24 13     4
  7Q GAIN WILD-TYPE 26 20     7
D14V5, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0                 24                26
  N1                 13                20
  N2+N3               4                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  7Q GAIN MUTATED   29   1  8
  7Q GAIN WILD-TYPE 46   0  7
D14V6, multiclass
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0               29                46
  M1A               1                 0
  MX                8                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    4 44
  7Q GAIN WILD-TYPE 11 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4   44
  7Q GAIN WILD-TYPE   11   46
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               4                11
  MALE                44                46
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   15 32
  7Q GAIN WILD-TYPE 20 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     15   32
  7Q GAIN WILD-TYPE   20   34
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN              15                20
  WHITE              32                34
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   23 15
  8P GAIN WILD-TYPE 44 16
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               38                60 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               15                16 
$`8P GAIN MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A8O2 
       33.27        20.09        20.78        17.03         0.36         0.46 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
      122.10        53.85         3.68         3.16         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OT 
        4.31         8.78         4.08        18.35         3.16         4.90 
TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K 
        7.13         2.60         0.36        21.37        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       10.45         0.33         0.13         0.07         0.10         0.07 
TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 
        0.10         0.10         0.10         7.59         5.06         7.04 
TCGA-RE-A7BO TCGA-V5-A7RE 
        7.00         4.80 

$`8P GAIN WILD-TYPE`
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-A6QS TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FB 
        0.53         0.79         0.13         1.12        44.75        60.39 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       41.52        42.77         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-A4OQ 
        3.35        19.50         6.41         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
       30.74        29.00         7.43         6.94         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-LN-A49M 
        7.40         3.95         3.02        16.47        83.24         0.16 
TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
        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-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6XG 
       17.62         5.16         3.78         8.02        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 

  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 
            4.195             4.555 
[1] "0.1 - 122.1 (4.2)" "0.0 - 83.2 (4.6)" 
[1] "hr=" "1.7"
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED         2        2        1        1        11         6
  8P GAIN WILD-TYPE       5        2        3        0        19        10
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED           6          1          2          2        1
  8P GAIN WILD-TYPE         5          7          4          1        0
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  2                 5
  STAGE IA                 2                 2
  STAGE IB                 1                 3
  STAGE II                 1                 0
  STAGE IIA               11                19
  STAGE IIB                6                10
  STAGE III                6                 5
  STAGE IIIA               1                 7
  STAGE IIIB               2                 4
  STAGE IIIC               2                 1
  STAGE IV                 1                 0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  8P GAIN MUTATED       9  5    22
  8P GAIN WILD-TYPE    10 21    28
D15V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1               9                10
  T2                  5                21
  T3+T4              22                28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  8P GAIN MUTATED   21 11     4
  8P GAIN WILD-TYPE 29 22     7
D15V5, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0                 21                29
  N1                 11                22
  N2+N3               4                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  8P GAIN MUTATED   27   1  6
  8P GAIN WILD-TYPE 48   0  9
D15V6, multiclass
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               27                48
  M1A               1                 0
  MX                6                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    6 34
  8P GAIN WILD-TYPE  9 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      6   34
  8P GAIN WILD-TYPE    9   56
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               6                 9
  MALE                34                56
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   15 24
  8P GAIN WILD-TYPE 20 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     15   24
  8P GAIN WILD-TYPE   20   42
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN              15                20
  WHITE              24                42
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   33 18
  8Q GAIN WILD-TYPE 34 13
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               51                47 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               18                13 
$`8Q GAIN MUTATED`
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-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE 
       17.03         0.36         0.46       122.10        53.85         3.68 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OM 
        3.16         3.45         0.30         4.31         8.78         4.08 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW 
       18.35         3.32         1.38         3.16         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K 
        7.43         2.60         0.36        21.37        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       10.45         0.33         0.10         0.13         0.07         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.07         0.10         0.10         0.10         0.07         0.10 
TCGA-LN-A5U6 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-RE-A7BO 
        0.20         7.59         5.06         7.04        53.95         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RE 
        8.78        14.01         4.80 

$`8Q GAIN WILD-TYPE`
TCGA-IG-A3Y9 TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A6QS 
        0.85         0.03         0.99         0.53         0.79         0.13 
TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC 
        1.12        44.75        60.39        41.52        42.77         6.21 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        8.94         3.52         3.68         3.35        19.50         6.41 
TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
        7.17        30.74        29.00         6.94         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-LN-A49M 
        7.40         3.95         3.02        16.47        83.24         0.16 
TCGA-LN-A49N TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.07         0.07         0.13         0.07         0.10         0.07 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.07         1.18        17.62         5.16         3.78         8.02 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-V5-A7RB 
       14.70        29.59         6.35         9.30         5.29 

  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 
             3.68              5.29 
[1] "0.1 - 122.1 (3.7)" "0.0 - 83.2 (5.3)" 
[1] "hr=" "1.5"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED         2        2        2        1        15         8
  8Q GAIN WILD-TYPE       5        2        2        0        15         8
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED           8          5          3          3        1
  8Q GAIN WILD-TYPE         3          3          3          0        0
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  2                 5
  STAGE IA                 2                 2
  STAGE IB                 2                 2
  STAGE II                 1                 0
  STAGE IIA               15                15
  STAGE IIB                8                 8
  STAGE III                8                 3
  STAGE IIIA               5                 3
  STAGE IIIB               3                 3
  STAGE IIIC               3                 0
  STAGE IV                 1                 0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  8Q GAIN MUTATED       9 11    31
  8Q GAIN WILD-TYPE    10 15    19
D16V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1               9                10
  T2                 11                15
  T3+T4              31                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  8Q GAIN MUTATED   26 18     7
  8Q GAIN WILD-TYPE 24 15     4
D16V5, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0                 26                24
  N1                 18                15
  N2+N3               7                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  8Q GAIN MUTATED   39   1  9
  8Q GAIN WILD-TYPE 36   0  6
D16V6, multiclass
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0               39                36
  M1A               1                 0
  MX                9                 6
[1] 3 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    6 50
  8Q GAIN WILD-TYPE  9 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6   50
  8Q GAIN WILD-TYPE    9   40
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               6                 9
  MALE                50                40
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   22 33
  8Q GAIN WILD-TYPE 13 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     22   33
  8Q GAIN WILD-TYPE   13   33
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN              22                13
  WHITE              33                33
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    6  1
  9P GAIN WILD-TYPE 61 30
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7                91 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                30 
$`9P GAIN MUTATED`
TCGA-IG-A625 TCGA-JY-A6F8 TCGA-L5-A4OU TCGA-L5-A88Y TCGA-L7-A6VZ TCGA-LN-A49O 
        0.36       122.10        29.00         0.36        10.36         0.33 
TCGA-LN-A49V 
        0.10 

$`9P GAIN WILD-TYPE`
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-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-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.13         1.12         0.46        44.75        60.39        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
        3.68        41.52        42.77         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-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49K 
        3.95         3.02        16.47        21.37        83.24         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-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-S8-A6BW TCGA-V5-A7RB 
       53.95         9.30         7.00         8.78        14.01         5.29 
TCGA-V5-A7RE 
        4.80 

  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 
             0.36              4.31 
[1] "0.1 - 122.1 (0.4)" "0.0 - 83.2 (4.3)" 
[1] "hr=" "3.4"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P GAIN MUTATED         1        0        0        0         4         0
  9P GAIN WILD-TYPE       6        4        4        1        26        16
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED           0          0          1          1        0
  9P GAIN WILD-TYPE        11          8          5          2        1
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  1                 6
  STAGE IA                 0                 4
  STAGE IB                 0                 4
  STAGE II                 0                 1
  STAGE IIA                4                26
  STAGE IIB                0                16
  STAGE III                0                11
  STAGE IIIA               0                 8
  STAGE IIIB               1                 5
  STAGE IIIC               1                 2
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  9P GAIN MUTATED       2  0     6
  9P GAIN WILD-TYPE    17 26    44
D17V4, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1               2                17
  T2                  0                26
  T3+T4               6                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  9P GAIN MUTATED    6  0     2
  9P GAIN WILD-TYPE 44 33     9
D17V5, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0                  6                44
  N1                  0                33
  N2+N3               2                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  9P GAIN MUTATED    6   0  2
  9P GAIN WILD-TYPE 69   1 13
D17V6, multiclass
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0                6                69
  M1A               0                 1
  MX                2                13
[1] 3 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    0  8
  9P GAIN WILD-TYPE 15 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0    8
  9P GAIN WILD-TYPE   15   82
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               0                15
  MALE                 8                82
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    4  4
  9P GAIN WILD-TYPE 31 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      4    4
  9P GAIN WILD-TYPE   31   62
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN               4                31
  WHITE               4                62
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED   16  2
  9Q GAIN WILD-TYPE 51 29
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               18                80 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                29 
$`9Q GAIN MUTATED`
TCGA-IG-A50L TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-L5-A43C TCGA-L5-A4OO 
        0.53         0.36       122.10        60.39         3.16         3.32 
TCGA-L5-A4OU TCGA-L5-A88Y TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49V 
       29.00         0.36        10.36         0.07         0.33         0.10 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-R6-A6L4 TCGA-S8-A6BV 
        0.10         0.13         0.07         0.10        14.70         8.78 

$`9Q GAIN WILD-TYPE`
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-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS 
        0.03         0.26         0.99        17.03         0.79         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        1.12         0.46        44.75        53.85         3.68        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       42.77         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-A8NJ TCGA-L5-A8NQ 
       25.12         7.40         3.95         3.02        16.47        21.37 
TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S 
       83.24        10.45         0.16         0.07         0.10         0.13 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.07         0.07         0.07         0.07         0.10         0.10 
TCGA-LN-A4A6 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-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 
        5.16         3.78         8.02         7.59         5.06         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 
        5.29         4.80 

  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 
            0.445             4.980 
[1] "0.1 - 122.1 (0.4)" "0.0 - 83.2 (5.0)" 
[1] "hr=" "3.2"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         2        0        0        0         8         0
  9Q GAIN WILD-TYPE       5        4        4        1        22        16
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED           1          2          1          2        0
  9Q GAIN WILD-TYPE        10          6          5          1        1
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  2                 5
  STAGE IA                 0                 4
  STAGE IB                 0                 4
  STAGE II                 0                 1
  STAGE IIA                8                22
  STAGE IIB                0                16
  STAGE III                1                10
  STAGE IIIA               2                 6
  STAGE IIIB               1                 5
  STAGE IIIC               2                 1
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  9Q GAIN MUTATED       3  1    13
  9Q GAIN WILD-TYPE    16 25    37
D18V4, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1               3                16
  T2                  1                25
  T3+T4              13                37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  9Q GAIN MUTATED   11  3     3
  9Q GAIN WILD-TYPE 39 30     8
D18V5, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0                 11                39
  N1                  3                30
  N2+N3               3                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  9Q GAIN MUTATED   14   0  3
  9Q GAIN WILD-TYPE 61   1 12
D18V6, multiclass
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0               14                61
  M1A               0                 1
  MX                3                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    0 19
  9Q GAIN WILD-TYPE 15 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   19
  9Q GAIN WILD-TYPE   15   71
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               0                15
  MALE                19                71
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   10  9
  9Q GAIN WILD-TYPE 25 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     10    9
  9Q GAIN WILD-TYPE   25   57
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN              10                25
  WHITE               9                57
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED   13  5
  10P GAIN WILD-TYPE 54 26
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                18                 80 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 5                 26 
$`10P GAIN MUTATED`
TCGA-IG-A3YC TCGA-JY-A6F8 TCGA-L5-A43C TCGA-L5-A4OH TCGA-L5-A4OR TCGA-L5-A88V 
       20.12       122.10         3.16        19.50         3.16         2.60 
TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49S 
        3.02        16.47        10.36        10.45         0.10         0.13 
TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-S8-A6BW 
        0.10         0.20         8.02         5.06         6.35        14.01 

$`10P GAIN WILD-TYPE`
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-A625 
        0.26         0.99         0.53        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.13         1.12         0.46        44.75        60.39        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
        3.68        41.52        42.77         6.21         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI 
        4.31         8.94         3.52         3.68         3.35         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-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-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NQ 
        8.71        25.12         0.36         7.40         3.95        21.37 
TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U 
       83.24         0.07         0.16         0.07         0.33         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-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-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-A7RE 
        5.29         4.80 

  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 
             5.705              4.015 
[1] "0.1 - 122.1 (5.7)" "0.0 - 83.2 (4.0)" 
[1] "hr=" "1.4"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P GAIN MUTATED         3        1        1        1         4         1
  10P GAIN WILD-TYPE       4        3        3        0        26        15
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED           3          1          0          1        0
  10P GAIN WILD-TYPE         8          7          6          2        1
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   3                  4
  STAGE IA                  1                  3
  STAGE IB                  1                  3
  STAGE II                  1                  0
  STAGE IIA                 4                 26
  STAGE IIB                 1                 15
  STAGE III                 3                  8
  STAGE IIIA                1                  7
  STAGE IIIB                0                  6
  STAGE IIIC                1                  2
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  10P GAIN MUTATED       4  5     7
  10P GAIN WILD-TYPE    15 21    43
D19V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1                4                 15
  T2                   5                 21
  T3+T4                7                 43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  10P GAIN MUTATED   10  5     1
  10P GAIN WILD-TYPE 40 28    10
D19V5, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                  10                 40
  N1                   5                 28
  N2+N3                1                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  10P GAIN MUTATED   12   0  4
  10P GAIN WILD-TYPE 63   1 11
D19V6, multiclass
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                12                 63
  M1A                0                  1
  MX                 4                 11
[1] 3 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    1 19
  10P GAIN WILD-TYPE 14 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1   19
  10P GAIN WILD-TYPE   14   71
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                1                 14
  MALE                 19                 71
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    7 13
  10P GAIN WILD-TYPE 28 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      7   13
  10P GAIN WILD-TYPE   28   53
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                7                 28
  WHITE               13                 53
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED    7  6
  10Q GAIN WILD-TYPE 60 25
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                13                 85 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 6                 25 
$`10Q GAIN MUTATED`
TCGA-IG-A5B8 TCGA-JY-A6F8 TCGA-L5-A43J TCGA-L5-A4OR TCGA-L5-A893 TCGA-L5-A8NJ 
        0.79       122.10         4.31         3.16         3.02        16.47 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49V TCGA-R6-A6KZ TCGA-R6-A6XQ 
       10.36        10.45         0.13         0.10         5.06         6.35 
TCGA-S8-A6BW 
       14.01 

$`10Q GAIN WILD-TYPE`
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-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 
        0.03         0.26         0.99         0.53        17.03         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.13         1.12         0.46        44.75        60.39        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
        3.68        41.52        42.77         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-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-A88Y TCGA-L5-A88Z 
        6.94         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
        3.95        21.37        83.24         0.07         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.33         0.10         0.07         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-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-A6L4 TCGA-R6-A6L6 
        5.16         3.78         8.02         7.59        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
       29.59        53.95         9.30         7.00         8.78         5.29 
TCGA-V5-A7RE 
        4.80 

  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 
              5.06               3.95 
[1] "0.1 - 122.1 (5.1)" "0.0 - 83.2 (4.0)" 
[1] "hr=" "1.4"
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q GAIN MUTATED         2        1        2        0         4         1
  10Q GAIN WILD-TYPE       5        3        2        1        26        15
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED           1          0          0          1        0
  10Q GAIN WILD-TYPE        10          8          6          2        1
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   2                  5
  STAGE IA                  1                  3
  STAGE IB                  2                  2
  STAGE II                  0                  1
  STAGE IIA                 4                 26
  STAGE IIB                 1                 15
  STAGE III                 1                 10
  STAGE IIIA                0                  8
  STAGE IIIB                0                  6
  STAGE IIIC                1                  2
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  10Q GAIN MUTATED       3  2     7
  10Q GAIN WILD-TYPE    16 24    43
D20V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T0+T1                3                 16
  T2                   2                 24
  T3+T4                7                 43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  10Q GAIN MUTATED   10  1     1
  10Q GAIN WILD-TYPE 40 32    10
D20V5, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                  10                 40
  N1                   1                 32
  N2+N3                1                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  10Q GAIN MUTATED    8   0  4
  10Q GAIN WILD-TYPE 67   1 11
D20V6, multiclass
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                 8                 67
  M1A                0                  1
  MX                 4                 11
[1] 3 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 13
  10Q GAIN WILD-TYPE 14 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1   13
  10Q GAIN WILD-TYPE   14   77
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                1                 14
  MALE                 13                 77
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    4 10
  10Q GAIN WILD-TYPE 31 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      4   10
  10Q GAIN WILD-TYPE   31   56
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                4                 31
  WHITE               10                 56
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED   12  6
  11P GAIN WILD-TYPE 55 25
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                18                 80 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                 25 
$`11P GAIN MUTATED`
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
      122.10        60.39         3.68         8.94         3.52         3.68 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-LN-A49V TCGA-LN-A49Y 
        4.08        18.35         1.38        29.00         0.10         0.07 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-RE-A7BO 
        0.10         0.07         3.78         7.59         7.04         7.00 

$`11P GAIN WILD-TYPE`
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-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-JY-A6FA TCGA-JY-A6FD 
        0.36         0.13         1.12         0.46        44.75        53.85 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       41.52        42.77         6.21         3.16         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO 
        4.31         3.35        19.50         8.78         6.41         3.32 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         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-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ 
        3.95         3.02        16.47        21.37        83.24        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-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.13         0.07         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-A5U6 
        0.10         0.10         0.10         0.07         0.07         0.20 
TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 
        1.18        17.62         5.16         8.02         5.06        14.70 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW 
       29.59         6.35        53.95         9.30         8.78        14.01 
TCGA-V5-A7RB TCGA-V5-A7RE 
        5.29         4.80 

  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 
             3.930              4.555 
[1] "0.1 - 122.1 (3.9)" "0.0 - 83.2 (4.6)" 
[1] "hr=" "1.1"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED         2        1        0        0         5         3
  11P GAIN WILD-TYPE       5        3        4        1        25        13
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           2          1          2          0        0
  11P GAIN WILD-TYPE         9          7          4          3        1
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   2                  5
  STAGE IA                  1                  3
  STAGE IB                  0                  4
  STAGE II                  0                  1
  STAGE IIA                 5                 25
  STAGE IIB                 3                 13
  STAGE III                 2                  9
  STAGE IIIA                1                  7
  STAGE IIIB                2                  4
  STAGE IIIC                0                  3
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  11P GAIN MUTATED       6  2     9
  11P GAIN WILD-TYPE    13 24    41
D21V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1                6                 13
  T2                   2                 24
  T3+T4                9                 41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  11P GAIN MUTATED    8  5     4
  11P GAIN WILD-TYPE 42 28     7
D21V5, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0                   8                 42
  N1                   5                 28
  N2+N3                4                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  11P GAIN MUTATED   11   0  2
  11P GAIN WILD-TYPE 64   1 13
D21V6, multiclass
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                11                 64
  M1A                0                  1
  MX                 2                 13
[1] 3 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    4 15
  11P GAIN WILD-TYPE 11 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      4   15
  11P GAIN WILD-TYPE   11   75
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                4                 11
  MALE                 15                 75
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    5 13
  11P GAIN WILD-TYPE 30 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5   13
  11P GAIN WILD-TYPE   30   53
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                5                 30
  WHITE               13                 53
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED   13  7
  11Q GAIN WILD-TYPE 54 24
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                20                 78 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                 24 
$`11Q GAIN MUTATED`
TCGA-IG-A51D TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-L5-A43M TCGA-L5-A4OE 
       17.03       122.10        60.39         3.68         8.94         3.52 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A88Y 
        3.68        19.50        18.35         1.38        29.00         0.36 
TCGA-LN-A49K TCGA-LN-A49Y TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-Q9-A6FW TCGA-R6-A6DQ 
        0.07         0.07         0.10         0.07         3.78         7.59 
TCGA-R6-A6L6 TCGA-RE-A7BO 
        7.04         7.00 

$`11Q GAIN WILD-TYPE`
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-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 
        0.03         0.26         0.99         0.53         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
        0.13         1.12         0.46        44.75        53.85        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       42.77         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-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       16.47        21.37        83.24        10.36        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-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-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 
        0.10         0.07         0.07         0.20         1.18        17.62 
TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ 
        5.16         8.02         5.06        14.70        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
       53.95         9.30         8.78        14.01         5.29         4.80 

  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 
             5.390              4.195 
[1] "0.1 - 122.1 (5.4)" "0.0 - 83.2 (4.2)" 
[1] "hr=" "1.1"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         3        0        0        0         4         4
  11Q GAIN WILD-TYPE       4        4        4        1        26        12
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           2          1          2          0        0
  11Q GAIN WILD-TYPE         9          7          4          3        1
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   3                  4
  STAGE IA                  0                  4
  STAGE IB                  0                  4
  STAGE II                  0                  1
  STAGE IIA                 4                 26
  STAGE IIB                 4                 12
  STAGE III                 2                  9
  STAGE IIIA                1                  7
  STAGE IIIB                2                  4
  STAGE IIIC                0                  3
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  11Q GAIN MUTATED       8  2     8
  11Q GAIN WILD-TYPE    11 24    42
D22V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1                8                 11
  T2                   2                 24
  T3+T4                8                 42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  11Q GAIN MUTATED    8  6     4
  11Q GAIN WILD-TYPE 42 27     7
D22V5, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                   8                 42
  N1                   6                 27
  N2+N3                4                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  11Q GAIN MUTATED   12   0  3
  11Q GAIN WILD-TYPE 63   1 12
D22V6, multiclass
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                12                 63
  M1A                0                  1
  MX                 3                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    3 17
  11Q GAIN WILD-TYPE 12 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3   17
  11Q GAIN WILD-TYPE   12   73
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                 12
  MALE                 17                 73
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    4 15
  11Q GAIN WILD-TYPE 31 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4   15
  11Q GAIN WILD-TYPE   31   51
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                4                 31
  WHITE               15                 51
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   24  9
  12P GAIN WILD-TYPE 43 22
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                33                 65 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 9                 22 
$`12P GAIN MUTATED`
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A8O2 TCGA-L5-A43H 
       20.09         2.63         0.03         0.53         0.46         0.30 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OT 
        4.31         3.52         8.78         4.08         3.32         4.90 
TCGA-L5-A88Y TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49R 
        0.36        21.37        10.36         0.07        10.45         0.10 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
        0.13         0.10         0.07         0.07         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.07         0.07         0.20         1.18         8.02         7.59 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-S8-A6BW 
       29.59        53.95        14.01 

$`12P GAIN WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
       33.27         0.85        20.78        20.12         0.26         0.99 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 
       17.03         0.79         0.36         0.13         1.12       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        53.85         3.68        41.52        42.77 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG 
        6.21         3.16         3.45         8.94         3.68         3.35 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       19.50         6.41        18.35         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-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ 
        2.60        25.12         7.40         3.95         3.02        16.47 
TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49X 
       83.24         0.16         0.07         0.33         0.07         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-M9-A5M8 
        0.07         0.13         0.10         0.07         0.10        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        5.16         3.78         5.06        14.70         7.04         6.35 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        9.30         7.00         8.78         5.29         4.80 

  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 
              1.18               6.21 
[1] "0.0 - 54.0 (1.2)"  "0.1 - 122.1 (6.2)"
[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         4
  12P GAIN WILD-TYPE       7        3        3        0        19        12
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           5          2          2          3        1
  12P GAIN WILD-TYPE         6          6          4          0        0
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   0                  7
  STAGE IA                  1                  3
  STAGE IB                  1                  3
  STAGE II                  1                  0
  STAGE IIA                11                 19
  STAGE IIB                 4                 12
  STAGE III                 5                  6
  STAGE IIIA                2                  6
  STAGE IIIB                2                  4
  STAGE IIIC                3                  0
  STAGE IV                  1                  0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  12P GAIN MUTATED       2 10    20
  12P GAIN WILD-TYPE    17 16    30
D23V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1                2                 17
  T2                  10                 16
  T3+T4               20                 30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  12P GAIN MUTATED   17 10     5
  12P GAIN WILD-TYPE 33 23     6
D23V5, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0                  17                 33
  N1                  10                 23
  N2+N3                5                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  12P GAIN MUTATED   24   1  5
  12P GAIN WILD-TYPE 51   0 10
D23V6, multiclass
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0                24                 51
  M1A                1                  0
  MX                 5                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    2 34
  12P GAIN WILD-TYPE 13 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2   34
  12P GAIN WILD-TYPE   13   56
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                2                 13
  MALE                 34                 56
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   18 18
  12P GAIN WILD-TYPE 17 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     18   18
  12P GAIN WILD-TYPE   17   48
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN               18                 17
  WHITE               18                 48
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED   17  3
  12Q GAIN WILD-TYPE 50 28
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                20                 78 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 28 
$`12Q GAIN MUTATED`
TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A8O2 TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4OO 
        2.63         0.53         0.46         3.52         4.08         3.32 
TCGA-L5-A4OT TCGA-L5-A88Y TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49V TCGA-LN-A49W 
        4.90         0.36        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 
        7.59        29.59 

$`12Q GAIN WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09         0.85        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-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        1.12       122.10        44.75        60.39        53.85         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       41.52        42.77         6.21         3.16         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-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
        6.41        18.35         7.17         1.38         3.16        30.74 
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-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NQ 
       25.12         7.40         3.95         3.02        16.47        21.37 
TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       83.24         0.07         0.16         0.07         0.33         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.13         0.07         0.10         0.07         0.13         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        0.10         0.10         0.07        17.62         5.16         3.78 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        8.02         5.06        14.70         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 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.07               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             29.59             122.10 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             0.855              5.750 
[1] "0.1 - 29.6 (0.9)"  "0.0 - 122.1 (5.8)"
[1] "hr=" "1.1"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED         0        1        0        1         6         1
  12Q GAIN WILD-TYPE       7        3        4        0        24        15
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED           2          2          2          2        1
  12Q GAIN WILD-TYPE         9          6          4          1        0
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   0                  7
  STAGE IA                  1                  3
  STAGE IB                  0                  4
  STAGE II                  1                  0
  STAGE IIA                 6                 24
  STAGE IIB                 1                 15
  STAGE III                 2                  9
  STAGE IIIA                2                  6
  STAGE IIIB                2                  4
  STAGE IIIC                2                  1
  STAGE IV                  1                  0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  12Q GAIN MUTATED       2  6    11
  12Q GAIN WILD-TYPE    17 20    39
D24V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1                2                 17
  T2                   6                 20
  T3+T4               11                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  12Q GAIN MUTATED    9  6     4
  12Q GAIN WILD-TYPE 41 27     7
D24V5, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                   9                 41
  N1                   6                 27
  N2+N3                4                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  12Q GAIN MUTATED   14   1  2
  12Q GAIN WILD-TYPE 61   0 13
D24V6, multiclass
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0                14                 61
  M1A                1                  0
  MX                 2                 13
[1] 3 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 19
  12Q GAIN WILD-TYPE 13 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   19
  12Q GAIN WILD-TYPE   13   71
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                2                 13
  MALE                 19                 71
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   12  9
  12Q GAIN WILD-TYPE 23 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     12    9
  12Q GAIN WILD-TYPE   23   57
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN               12                 23
  WHITE                9                 57
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED   16  7
  13Q GAIN WILD-TYPE 51 24
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                23                 75 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 7                 24 
$`13Q GAIN MUTATED`
TCGA-IG-A5B8 TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43E 
        0.79       122.10         3.68        42.77         3.16         3.45 
TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OW 
        8.94         3.35         8.78         7.17         1.38         7.13 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-Q9-A6FW 
        2.60         0.36         3.02         0.10         1.18         3.78 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-V5-A7RB 
       14.70         7.04         9.30         8.78         5.29 

$`13Q GAIN WILD-TYPE`
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-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 
        0.03         0.26         0.99         0.53        17.03         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.13         1.12         0.46        44.75        60.39        53.85 
TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF 
       41.52         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-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU 
       25.12         7.40         3.95        16.47        21.37        83.24 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         0.07        10.45         0.16         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-A4MR TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.07         0.07         0.07         0.20        17.62         5.16 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        8.02         7.59         5.06        29.59         6.35        53.95 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE 
        7.00        14.01         4.80 

  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 
              3.78               4.31 
[1] "0.1 - 122.1 (3.8)" "0.0 - 83.2 (4.3)" 
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q GAIN MUTATED         4        1        1        0         3         2
  13Q GAIN WILD-TYPE       3        3        3        1        27        14
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED           3          2          1          1        0
  13Q GAIN WILD-TYPE         8          6          5          2        1
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   4                  3
  STAGE IA                  1                  3
  STAGE IB                  1                  3
  STAGE II                  0                  1
  STAGE IIA                 3                 27
  STAGE IIB                 2                 14
  STAGE III                 3                  8
  STAGE IIIA                2                  6
  STAGE IIIB                1                  5
  STAGE IIIC                1                  2
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  13Q GAIN MUTATED       7  5     9
  13Q GAIN WILD-TYPE    12 21    41
D25V4, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1                7                 12
  T2                   5                 21
  T3+T4                9                 41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  13Q GAIN MUTATED   10  7     4
  13Q GAIN WILD-TYPE 40 26     7
D25V5, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0                  10                 40
  N1                   7                 26
  N2+N3                4                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  13Q GAIN MUTATED   13   0  8
  13Q GAIN WILD-TYPE 62   1  7
D25V6, multiclass
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0                13                 62
  M1A                0                  1
  MX                 8                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    5 20
  13Q GAIN WILD-TYPE 10 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5   20
  13Q GAIN WILD-TYPE   10   70
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                5                 10
  MALE                 20                 70
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    4 18
  13Q GAIN WILD-TYPE 31 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4   18
  13Q GAIN WILD-TYPE   31   48
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                4                 31
  WHITE               18                 48
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED   16  8
  14Q GAIN WILD-TYPE 51 23
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                24                 74 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                 23 
$`14Q GAIN MUTATED`
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A6QS TCGA-L5-A43C TCGA-L5-A43E 
        0.85        20.78         0.03         0.13         3.16         3.45 
TCGA-L5-A43J TCGA-L5-A4OR TCGA-L5-A4OX TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49S 
        4.31         3.16         7.43        21.37         0.07         0.13 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A4MR 
        0.07         0.10         0.10         0.10         0.07         0.07 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6Y0 TCGA-S8-A6BV TCGA-S8-A6BW 
        0.20         1.18         8.02        53.95         8.78        14.01 

$`14Q GAIN WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
       33.27        20.09         2.63        20.12         0.26         0.99 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
        0.53        17.03         0.79         0.36         1.12         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        53.85         3.68        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       42.77         6.21         0.30         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-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.13         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L7-A6VZ 
        7.40         3.95         3.02        16.47        83.24        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W 
       10.45         0.16         0.07         0.33         0.10         0.07 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.07         0.13         0.07         0.10         0.10         0.07 
TCGA-LN-A4MQ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.10        17.62         5.16         3.78         7.59         5.06 
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-V5-A7RB TCGA-V5-A7RE 
        5.29         4.80 

  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 
             1.015              5.225 
[1] "0.0 - 54.0 (1.0)"  "0.1 - 122.1 (5.2)"
[1] "hr=" "1.8"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         1        1        1        0        11         5
  14Q GAIN WILD-TYPE       6        3        3        1        19        11
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED           2          3          0          0        0
  14Q GAIN WILD-TYPE         9          5          6          3        1
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   1                  6
  STAGE IA                  1                  3
  STAGE IB                  1                  3
  STAGE II                  0                  1
  STAGE IIA                11                 19
  STAGE IIB                 5                 11
  STAGE III                 2                  9
  STAGE IIIA                3                  5
  STAGE IIIB                0                  6
  STAGE IIIC                0                  3
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  14Q GAIN MUTATED       2 10    12
  14Q GAIN WILD-TYPE    17 16    38
D26V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1                2                 17
  T2                  10                 16
  T3+T4               12                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  14Q GAIN MUTATED   17  7     0
  14Q GAIN WILD-TYPE 33 26    11
D26V5, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0                  17                 33
  N1                   7                 26
  N2+N3                0                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  14Q GAIN MUTATED   20   0  4
  14Q GAIN WILD-TYPE 55   1 11
D26V6, multiclass
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                20                 55
  M1A                0                  1
  MX                 4                 11
[1] 3 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 27
  14Q GAIN WILD-TYPE 15 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   27
  14Q GAIN WILD-TYPE   15   63
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                0                 15
  MALE                 27                 63
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   13 14
  14Q GAIN WILD-TYPE 22 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     13   14
  14Q GAIN WILD-TYPE   22   52
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN               13                 22
  WHITE               14                 52
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED   12  6
  15Q GAIN WILD-TYPE 55 25
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                18                 80 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                 25 
$`15Q GAIN MUTATED`
TCGA-IG-A50L TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-L5-A43C TCGA-L5-A4OR TCGA-L5-A4OW 
        0.53       122.10        60.39         3.16         3.16         7.13 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NJ TCGA-LN-A49L TCGA-LN-A49R 
        6.94         2.60         0.36        16.47        10.45         0.10 
TCGA-LN-A4MR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ 
        0.07        17.62         3.78         7.59         7.04         6.35 

$`15Q GAIN WILD-TYPE`
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-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-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        0.13         1.12         0.46        44.75        53.85         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       41.52        42.77         6.21         3.45         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-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W 
       30.74         4.90        29.00         7.43         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ 
        7.40         3.95         3.02        21.37        83.24        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-A7RE 
        5.29         4.80 

  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 
             6.645              4.015 
[1] "0.1 - 122.1 (6.6)" "0.0 - 83.2 (4.0)" 
[1] "hr=" "1.1"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q GAIN MUTATED         2        1        1        0         5         1
  15Q GAIN WILD-TYPE       5        3        3        1        25        15
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           3          1          1          0        0
  15Q GAIN WILD-TYPE         8          7          5          3        1
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   2                  5
  STAGE IA                  1                  3
  STAGE IB                  1                  3
  STAGE II                  0                  1
  STAGE IIA                 5                 25
  STAGE IIB                 1                 15
  STAGE III                 3                  8
  STAGE IIIA                1                  7
  STAGE IIIB                1                  5
  STAGE IIIC                0                  3
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  15Q GAIN MUTATED       4  5     7
  15Q GAIN WILD-TYPE    15 21    43
D27V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1                4                 15
  T2                   5                 21
  T3+T4                7                 43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  15Q GAIN MUTATED   10  5     1
  15Q GAIN WILD-TYPE 40 28    10
D27V5, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                  10                 40
  N1                   5                 28
  N2+N3                1                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  15Q GAIN MUTATED   12   0  4
  15Q GAIN WILD-TYPE 63   1 11
D27V6, multiclass
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                12                 63
  M1A                0                  1
  MX                 4                 11
[1] 3 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 18
  15Q GAIN WILD-TYPE 13 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2   18
  15Q GAIN WILD-TYPE   13   72
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                2                 13
  MALE                 18                 72
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    6 12
  15Q GAIN WILD-TYPE 29 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      6   12
  15Q GAIN WILD-TYPE   29   54
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                6                 29
  WHITE               12                 54
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED   14  6
  16P GAIN WILD-TYPE 53 25
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                20                 78 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                 25 
$`16P GAIN MUTATED`
TCGA-IG-A3Y9 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A43H TCGA-L5-A4OO TCGA-L5-A4OU 
        0.85         0.53         0.79         0.30         3.32        29.00 
TCGA-L5-A88S TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49W 
        6.94        21.37        10.36         0.07         0.13         0.07 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-R6-A6KZ 
        0.07         0.10         0.10         0.07         0.20         5.06 
TCGA-R6-A6XG TCGA-S8-A6BW 
       29.59        14.01 

$`16P GAIN WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09        20.78         2.63        20.12         0.03 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.26         0.99        17.03         0.36         0.13         1.12 
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        53.85         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J 
       41.52        42.77         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-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-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
       30.74         4.90         7.13         7.43         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ 
       25.12         0.36         7.40         3.95         3.02        16.47 
TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       83.24        10.45         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-A4A5 
        0.07         0.10         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-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        3.78         8.02         7.59        14.70         7.04         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 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.07               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             29.59             122.10 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.66               5.03 
[1] "0.1 - 29.6 (0.7)"  "0.0 - 122.1 (5.0)"
[1] "hr=" "1.5"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED         0        0        3        1         6         1
  16P GAIN WILD-TYPE       7        4        1        0        24        15
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           5          2          0          2        0
  16P GAIN WILD-TYPE         6          6          6          1        1
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   0                  7
  STAGE IA                  0                  4
  STAGE IB                  3                  1
  STAGE II                  1                  0
  STAGE IIA                 6                 24
  STAGE IIB                 1                 15
  STAGE III                 5                  6
  STAGE IIIA                2                  6
  STAGE IIIB                0                  6
  STAGE IIIC                2                  1
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  16P GAIN MUTATED       0  5    15
  16P GAIN WILD-TYPE    19 21    35
D28V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1                0                 19
  T2                   5                 21
  T3+T4               15                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  16P GAIN MUTATED   11  7     2
  16P GAIN WILD-TYPE 39 26     9
D28V5, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0                  11                 39
  N1                   7                 26
  N2+N3                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  16P GAIN MUTATED   17   0  3
  16P GAIN WILD-TYPE 58   1 12
D28V6, multiclass
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                17                 58
  M1A                0                  1
  MX                 3                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    0 22
  16P GAIN WILD-TYPE 15 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   22
  16P GAIN WILD-TYPE   15   68
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                0                 15
  MALE                 22                 68
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   11 11
  16P GAIN WILD-TYPE 24 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     11   11
  16P GAIN WILD-TYPE   24   55
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN               11                 24
  WHITE               11                 55
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   11  5
  16Q GAIN WILD-TYPE 56 26
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                16                 82 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                 26 
$`16Q GAIN MUTATED`
TCGA-IG-A3Y9 TCGA-IG-A5B8 TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OO TCGA-L5-A4OU 
        0.85         0.79         0.30         4.31         3.32        29.00 
TCGA-L5-A88S TCGA-L5-A8NQ TCGA-LN-A49R TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
        6.94        21.37         0.10         0.07         0.10         0.10 
TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-R6-A6XG TCGA-S8-A6BW 
        0.07         0.20        29.59        14.01 

$`16Q GAIN WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09        20.78         2.63        20.12         0.03 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
        0.26         0.99         0.53        17.03         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        1.12         0.46       122.10        44.75        60.39        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
        3.68        41.52        42.77         6.21         3.16         3.45 
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-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-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
       30.74         4.90         7.13         7.43         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ 
       25.12         0.36         7.40         3.95         3.02        16.47 
TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       83.24        10.36         0.07        10.45         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.33         0.13         0.07         0.10         0.07         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.07         0.13         0.10         0.07         0.10         0.07 
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-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        14.70         7.04         6.35        53.95         9.30 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        7.00         8.78         5.29         4.80 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.07               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             29.59             122.10 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.82               4.98 
[1] "0.1 - 29.6 (0.8)"  "0.0 - 122.1 (5.0)"
[1] "hr=" "1.5"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED         0        0        3        1         4         2
  16Q GAIN WILD-TYPE       7        4        1        0        26        14
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED           5          1          0          1        0
  16Q GAIN WILD-TYPE         6          7          6          2        1
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   0                  7
  STAGE IA                  0                  4
  STAGE IB                  3                  1
  STAGE II                  1                  0
  STAGE IIA                 4                 26
  STAGE IIB                 2                 14
  STAGE III                 5                  6
  STAGE IIIA                1                  7
  STAGE IIIB                0                  6
  STAGE IIIC                1                  2
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  16Q GAIN MUTATED       0  5    12
  16Q GAIN WILD-TYPE    19 21    38
D29V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1                0                 19
  T2                   5                 21
  T3+T4               12                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  16Q GAIN MUTATED   10  6     1
  16Q GAIN WILD-TYPE 40 27    10
D29V5, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0                  10                 40
  N1                   6                 27
  N2+N3                1                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  16Q GAIN MUTATED   14   0  3
  16Q GAIN WILD-TYPE 61   1 12
D29V6, multiclass
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                14                 61
  M1A                0                  1
  MX                 3                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    0 18
  16Q GAIN WILD-TYPE 15 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   18
  16Q GAIN WILD-TYPE   15   72
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                0                 15
  MALE                 18                 72
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    8 10
  16Q GAIN WILD-TYPE 27 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      8   10
  16Q GAIN WILD-TYPE   27   56
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                8                 27
  WHITE               10                 56
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED   10  7
  17P GAIN WILD-TYPE 57 24
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                17                 81 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 7                 24 
$`17P GAIN MUTATED`
TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-JY-A6FB TCGA-L5-A43H 
       20.09         0.53        17.03         0.36        60.39         0.30 
TCGA-L5-A43J TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A88Z TCGA-LN-A49O TCGA-LN-A49R 
        4.31        18.35         1.38         7.40         0.33         0.10 
TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-R6-A6DN TCGA-R6-A6KZ 
        0.10         0.13         0.10         8.02         5.06 

$`17P GAIN WILD-TYPE`
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-A5B8 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.26         0.99         0.79         0.13         1.12         0.46 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        53.85         3.68        41.52        42.77 
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-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ 
        3.95         3.02        16.47        21.37        83.24        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 
       14.01         5.29         4.80 

  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 
              1.38               4.80 
[1] "0.1 - 60.4 (1.4)"  "0.0 - 122.1 (4.8)"
[1] "hr=" "1.8"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         1        0        0        0         5         4
  17P GAIN WILD-TYPE       6        4        4        1        25        12
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED           3          2          1          0        0
  17P GAIN WILD-TYPE         8          6          5          3        1
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   1                  6
  STAGE IA                  0                  4
  STAGE IB                  0                  4
  STAGE II                  0                  1
  STAGE IIA                 5                 25
  STAGE IIB                 4                 12
  STAGE III                 3                  8
  STAGE IIIA                2                  6
  STAGE IIIB                1                  5
  STAGE IIIC                0                  3
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  17P GAIN MUTATED       4  2    10
  17P GAIN WILD-TYPE    15 24    40
D30V4, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1                4                 15
  T2                   2                 24
  T3+T4               10                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  17P GAIN MUTATED    7  7     2
  17P GAIN WILD-TYPE 43 26     9
D30V5, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                   7                 43
  N1                   7                 26
  N2+N3                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  17P GAIN MUTATED   13   0  2
  17P GAIN WILD-TYPE 62   1 13
D30V6, multiclass
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                13                 62
  M1A                0                  1
  MX                 2                 13
[1] 3 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 17
  17P GAIN WILD-TYPE 14 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   17
  17P GAIN WILD-TYPE   14   73
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                1                 14
  MALE                 17                 73
[1] 2 2
[1] FALSE
D30V8, continuous
D30V9, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    8 10
  17P GAIN WILD-TYPE 27 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      8   10
  17P GAIN WILD-TYPE   27   56
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                8                 27
  WHITE               10                 56
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED   15  8
  17Q GAIN WILD-TYPE 52 23
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                23                 75 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 8                 23 
$`17Q GAIN MUTATED`
TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-JY-A6FB TCGA-L5-A43E 
       20.09         0.53        17.03         0.36        60.39         3.45 
TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OT 
        0.30         3.52        18.35         3.32         1.38         4.90 
TCGA-L5-A88Z TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A3 
        7.40         0.10         0.13         0.10         0.13         0.07 
TCGA-LN-A4A4 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG 
        0.10         8.02         7.59         5.06        29.59 

$`17Q GAIN WILD-TYPE`
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-A5B8 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.26         0.99         0.79         0.13         1.12         0.46 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        53.85         3.68        41.52        42.77 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG 
        6.21         3.16         4.31         8.94         3.68         3.35 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR 
       19.50         8.78         6.41         4.08         7.17         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-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ 
        2.60        25.12         0.36         3.95         3.02        16.47 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       21.37        83.24        10.36         0.07        10.45         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.07         0.33         0.07         0.07         0.10         0.07 
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-A6L4 
        0.20         1.18        17.62         5.16         3.78        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-A7RE 
       14.01         5.29         4.80 

  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 
              3.45               4.80 
[1] "0.1 - 60.4 (3.5)"  "0.0 - 122.1 (4.8)"
[1] "hr=" "1.5"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED         2        0        0        0         5         3
  17Q GAIN WILD-TYPE       5        4        4        1        25        13
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED           4          2          2          1        1
  17Q GAIN WILD-TYPE         7          6          4          2        0
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   2                  5
  STAGE IA                  0                  4
  STAGE IB                  0                  4
  STAGE II                  0                  1
  STAGE IIA                 5                 25
  STAGE IIB                 3                 13
  STAGE III                 4                  7
  STAGE IIIA                2                  6
  STAGE IIIB                2                  4
  STAGE IIIC                1                  2
  STAGE IV                  1                  0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  17Q GAIN MUTATED       5  2    13
  17Q GAIN WILD-TYPE    14 24    37
D31V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1                5                 14
  T2                   2                 24
  T3+T4               13                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  17Q GAIN MUTATED    7  9     4
  17Q GAIN WILD-TYPE 43 24     7
D31V5, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0                   7                 43
  N1                   9                 24
  N2+N3                4                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  17Q GAIN MUTATED   16   1  1
  17Q GAIN WILD-TYPE 59   0 14
D31V6, multiclass
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0                16                 59
  M1A                1                  0
  MX                 1                 14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    2 22
  17Q GAIN WILD-TYPE 13 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2   22
  17Q GAIN WILD-TYPE   13   68
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                2                 13
  MALE                 22                 68
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    9 15
  17Q GAIN WILD-TYPE 26 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      9   15
  17Q GAIN WILD-TYPE   26   51
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                9                 26
  WHITE               15                 51
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED   18 11
  18P GAIN WILD-TYPE 49 20
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                29                 69 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                11                 20 
$`18P GAIN MUTATED`
TCGA-IG-A50L TCGA-IG-A625 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-L5-A43J TCGA-L5-A43M 
        0.53         0.36        60.39         3.68         4.31         8.94 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW 
        4.08        18.35         1.38         3.16         4.90         7.13 
TCGA-L5-A88Y TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
        0.36        21.37        83.24         0.13         0.07         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.07         0.10         0.07         0.10         0.10         0.07 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6KZ TCGA-S8-A6BW TCGA-V5-A7RE 
        0.20         1.18         5.06        14.01         4.80 

$`18P GAIN WILD-TYPE`
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-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS 
        0.03         0.26         0.99        17.03         0.79         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
        1.12         0.46       122.10        44.75        53.85        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE 
       42.77         6.21         3.16         3.45         0.30         3.52 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO 
        3.68         3.35        19.50         8.78         6.41         3.32 
TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        7.17        30.74        29.00         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ 
        2.60        25.12         7.40         3.95         3.02        16.47 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         0.07        10.45         0.16         0.07         0.33 
TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.10         0.07         0.13         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.07        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 
        7.00         8.78         5.29 

  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 
              1.38               6.35 
[1] "0.1 - 83.2 (1.4)"  "0.0 - 122.1 (6.3)"
[1] "hr=" "1.9"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED         1        2        2        0         8         4
  18P GAIN WILD-TYPE       6        2        2        1        22        12
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED           5          2          1          0        1
  18P GAIN WILD-TYPE         6          6          5          3        0
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   1                  6
  STAGE IA                  2                  2
  STAGE IB                  2                  2
  STAGE II                  0                  1
  STAGE IIA                 8                 22
  STAGE IIB                 4                 12
  STAGE III                 5                  6
  STAGE IIIA                2                  6
  STAGE IIIB                1                  5
  STAGE IIIC                0                  3
  STAGE IV                  1                  0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  18P GAIN MUTATED       6  8    14
  18P GAIN WILD-TYPE    13 18    36
D32V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1                6                 13
  T2                   8                 18
  T3+T4               14                 36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  18P GAIN MUTATED   15 10     3
  18P GAIN WILD-TYPE 35 23     8
D32V5, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                  15                 35
  N1                  10                 23
  N2+N3                3                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  18P GAIN MUTATED   19   1  6
  18P GAIN WILD-TYPE 56   0  9
D32V6, multiclass
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                19                 56
  M1A                1                  0
  MX                 6                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    3 26
  18P GAIN WILD-TYPE 12 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3   26
  18P GAIN WILD-TYPE   12   64
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                3                 12
  MALE                 26                 64
[1] 2 2
[1] FALSE
D32V8, continuous
D32V9, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   13 14
  18P GAIN WILD-TYPE 22 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     13   14
  18P GAIN WILD-TYPE   22   52
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN               13                 22
  WHITE               14                 52
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    7  7
  18Q GAIN WILD-TYPE 60 24
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                14                 84 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 7                 24 
$`18Q GAIN MUTATED`
TCGA-IG-A3I8 TCGA-IG-A625 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-L5-A43E TCGA-L5-A4OR 
       33.27         0.36        60.39         3.68         3.45         3.16 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A8NQ TCGA-LN-A49X TCGA-LN-A4A3 
        4.90         7.13         0.36        21.37         0.10         0.07 
TCGA-R6-A6KZ TCGA-S8-A6BW 
        5.06        14.01 

$`18Q GAIN WILD-TYPE`
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-A6QS 
        0.26         0.99         0.53        17.03         0.79         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
        1.12         0.46       122.10        44.75        53.85        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       42.77         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-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-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-A8NJ TCGA-L5-A8NU TCGA-L7-A6VZ 
        7.40         3.95         3.02        16.47        83.24        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-A49Y TCGA-LN-A4A2 
        0.13         0.07         0.10         0.07         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-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-V5-A7RB TCGA-V5-A7RE 
       53.95         9.30         7.00         8.78         5.29         4.80 

  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 
             4.290              4.195 
[1] "0.1 - 60.4 (4.3)"  "0.0 - 122.1 (4.2)"
[1] "hr=" "1.8"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         2        1        1        0         3         1
  18Q GAIN WILD-TYPE       5        3        3        1        27        15
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED           3          0          1          0        1
  18Q GAIN WILD-TYPE         8          8          5          3        0
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   2                  5
  STAGE IA                  1                  3
  STAGE IB                  1                  3
  STAGE II                  0                  1
  STAGE IIA                 3                 27
  STAGE IIB                 1                 15
  STAGE III                 3                  8
  STAGE IIIA                0                  8
  STAGE IIIB                1                  5
  STAGE IIIC                0                  3
  STAGE IV                  1                  0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  18Q GAIN MUTATED       4  3     7
  18Q GAIN WILD-TYPE    15 23    43
D33V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1                4                 15
  T2                   3                 23
  T3+T4                7                 43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  18Q GAIN MUTATED    8  5     1
  18Q GAIN WILD-TYPE 42 28    10
D33V5, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                   8                 42
  N1                   5                 28
  N2+N3                1                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  18Q GAIN MUTATED   10   1  3
  18Q GAIN WILD-TYPE 65   0 12
D33V6, multiclass
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                10                 65
  M1A                1                  0
  MX                 3                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    2 13
  18Q GAIN WILD-TYPE 13 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   13
  18Q GAIN WILD-TYPE   13   77
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                2                 13
  MALE                 13                 77
[1] 2 2
[1] FALSE
D33V8, continuous
D33V9, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    4 10
  18Q GAIN WILD-TYPE 31 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4   10
  18Q GAIN WILD-TYPE   31   56
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                4                 31
  WHITE               10                 56
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED    9  3
  19P GAIN WILD-TYPE 58 28
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                12                 86 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                 28 
$`19P GAIN MUTATED`
TCGA-IG-A3QL TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       20.09         3.16         3.52         3.32         1.38         3.16 
TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A5U7 TCGA-R6-A6XG TCGA-S8-A6BW 
        0.07         0.13         0.10         1.18        29.59        14.01 

$`19P GAIN WILD-TYPE`
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-A625 
        0.26         0.99         0.53        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
        0.13         1.12         0.46       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43E 
       53.85         3.68        41.52        42.77         6.21         3.45 
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-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-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       16.47        21.37        83.24        10.36        10.45         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
        0.07         0.33         0.10         0.07         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-M9-A5M8 
        0.07         0.07         0.10         0.07         0.20        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-A7RE 
        5.29         4.80 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.07               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             29.59             122.10 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              3.16               4.98 
[1] "0.1 - 29.6 (3.2)"  "0.0 - 122.1 (5.0)"
[1] "hr=" "1.1"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED         0        1        1        0         5         1
  19P GAIN WILD-TYPE       7        3        3        1        25        15
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           0          1          1          1        0
  19P GAIN WILD-TYPE        11          7          5          2        1
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   0                  7
  STAGE IA                  1                  3
  STAGE IB                  1                  3
  STAGE II                  0                  1
  STAGE IIA                 5                 25
  STAGE IIB                 1                 15
  STAGE III                 0                 11
  STAGE IIIA                1                  7
  STAGE IIIB                1                  5
  STAGE IIIC                1                  2
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  19P GAIN MUTATED       1  4     6
  19P GAIN WILD-TYPE    18 22    44
D34V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1                1                 18
  T2                   4                 22
  T3+T4                6                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  19P GAIN MUTATED    8  0     3
  19P GAIN WILD-TYPE 42 33     8
D34V5, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                   8                 42
  N1                   0                 33
  N2+N3                3                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  19P GAIN MUTATED    7   0  3
  19P GAIN WILD-TYPE 68   1 12
D34V6, multiclass
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                 7                 68
  M1A                0                  1
  MX                 3                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    0 13
  19P GAIN WILD-TYPE 15 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   13
  19P GAIN WILD-TYPE   15   77
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                0                 15
  MALE                 13                 77
[1] 2 2
[1] FALSE
D34V8, continuous
D34V9, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    5  8
  19P GAIN WILD-TYPE 30 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      5    8
  19P GAIN WILD-TYPE   30   58
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                5                 30
  WHITE                8                 58
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   13  5
  19Q GAIN WILD-TYPE 54 26
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                18                 80 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 5                 26 
$`19Q GAIN MUTATED`
TCGA-IG-A3QL TCGA-IG-A4QS TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH 
       20.09         0.26         3.16         3.52         3.68        19.50 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49U 
        3.32         1.38         3.16        10.36         0.07         0.07 
TCGA-LN-A4A6 TCGA-LN-A5U7 TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-S8-A6BW 
        0.10         1.18         5.06        14.70        29.59        14.01 

$`19Q GAIN WILD-TYPE`
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-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-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        1.12         0.46       122.10        44.75        60.39        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
        3.68        41.52        42.77         6.21         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        4.31         8.94         3.35         8.78         6.41         4.08 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
       18.35         7.17        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-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU 
        7.40         3.95         3.02        16.47        21.37        83.24 
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-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-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-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.20        17.62         5.16         3.78         8.02         7.59 
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-A7RE 
        5.29         4.80 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.07               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             29.59             122.10 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              3.42               4.85 
[1] "0.1 - 29.6 (3.4)"  "0.0 - 122.1 (4.8)"
[1] "hr=" "1.1"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED         1        1        1        1         4         2
  19Q GAIN WILD-TYPE       6        3        3        0        26        14
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           0          1          2          2        0
  19Q GAIN WILD-TYPE        11          7          4          1        1
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   1                  6
  STAGE IA                  1                  3
  STAGE IB                  1                  3
  STAGE II                  1                  0
  STAGE IIA                 4                 26
  STAGE IIB                 2                 14
  STAGE III                 0                 11
  STAGE IIIA                1                  7
  STAGE IIIB                2                  4
  STAGE IIIC                2                  1
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  19Q GAIN MUTATED       3  5     7
  19Q GAIN WILD-TYPE    16 21    43
D35V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1                3                 16
  T2                   5                 21
  T3+T4                7                 43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  19Q GAIN MUTATED    9  1     5
  19Q GAIN WILD-TYPE 41 32     6
D35V5, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                   9                 41
  N1                   1                 32
  N2+N3                5                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  19Q GAIN MUTATED    9   0  4
  19Q GAIN WILD-TYPE 66   1 11
D35V6, multiclass
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0                 9                 66
  M1A                0                  1
  MX                 4                 11
[1] 3 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    0 19
  19Q GAIN WILD-TYPE 15 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0   19
  19Q GAIN WILD-TYPE   15   71
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                0                 15
  MALE                 19                 71
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    5 14
  19Q GAIN WILD-TYPE 30 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      5   14
  19Q GAIN WILD-TYPE   30   52
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                5                 30
  WHITE               14                 52
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   33 18
  20P GAIN WILD-TYPE 34 13
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                51                 47 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                18                 13 
$`20P GAIN MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
       33.27        20.09         0.85         2.63        20.12         0.26 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-L5-A43C 
        0.53        17.03         0.46       122.10         3.68         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OM 
        3.45         0.30         4.31         3.52         3.35         4.08 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
       18.35         1.38        30.74         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NJ 
        7.43         6.94         2.60         0.36         7.40        16.47 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A4A2 
       10.36        10.45         0.10         0.13         0.10         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6DN 
        0.07         0.10         0.07         0.20         1.18         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 
        7.59         5.06        14.70         7.04         6.35         9.30 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        8.78         5.29         4.80 

$`20P GAIN WILD-TYPE`
TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
       20.78         0.03         0.99         0.79         0.36         0.13 
TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH 
        1.12        44.75        60.39        53.85        41.52        42.77 
TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        6.21         8.94         3.68        19.50         8.78         6.41 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A891 
        3.32         7.17         3.16         8.71        25.12         3.95 
TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
        3.02        21.37        83.24         0.07         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A4 
        0.33         0.07         0.10         0.07         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.10         0.07         0.10         0.07        17.62         5.16 
TCGA-Q9-A6FW TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BW 
        3.78        29.59        53.95         7.00        14.01 

  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 
              4.80               3.78 
[1] "0.1 - 122.1 (4.8)" "0.0 - 83.2 (3.8)" 
[1] "hr=" "1.5"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED         3        1        2        1        12         8
  20P GAIN WILD-TYPE       4        3        2        0        18         8
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED           6          6          3          1        1
  20P GAIN WILD-TYPE         5          2          3          2        0
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   3                  4
  STAGE IA                  1                  3
  STAGE IB                  2                  2
  STAGE II                  1                  0
  STAGE IIA                12                 18
  STAGE IIB                 8                  8
  STAGE III                 6                  5
  STAGE IIIA                6                  2
  STAGE IIIB                3                  3
  STAGE IIIC                1                  2
  STAGE IV                  1                  0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  20P GAIN MUTATED      10 11    25
  20P GAIN WILD-TYPE     9 15    25
D36V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1               10                  9
  T2                  11                 15
  T3+T4               25                 25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  20P GAIN MUTATED   22 19     5
  20P GAIN WILD-TYPE 28 14     6
D36V5, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0                  22                 28
  N1                  19                 14
  N2+N3                5                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  20P GAIN MUTATED   34   1  8
  20P GAIN WILD-TYPE 41   0  7
D36V6, multiclass
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0                34                 41
  M1A                1                  0
  MX                 8                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    7 47
  20P GAIN WILD-TYPE  8 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7   47
  20P GAIN WILD-TYPE    8   43
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                7                  8
  MALE                 47                 43
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   15 37
  20P GAIN WILD-TYPE 20 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     15   37
  20P GAIN WILD-TYPE   20   29
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN               15                 20
  WHITE               37                 29
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   36 21
  20Q GAIN WILD-TYPE 31 10
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                57                 41 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                21                 10 
$`20Q GAIN MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L 
       33.27         0.85         2.63        20.12         0.26         0.53 
TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-L5-A43C TCGA-L5-A43E 
       17.03         0.46       122.10         3.68         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         4.31         3.52         3.68         3.35        19.50 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        4.08        18.35         1.38         3.16        30.74         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y 
       29.00         7.13         7.43         6.94         2.60         0.36 
TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R 
        7.40        16.47        21.37        10.36        10.45         0.10 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
        0.13         0.10         0.10         0.13         0.07         0.10 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.20         1.18         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-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        8.78         5.29         4.80 

$`20Q GAIN WILD-TYPE`
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 
       20.09        20.78         0.03         0.99         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG 
        0.13         1.12        44.75        60.39        53.85        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO 
       42.77         6.21         8.94         8.78         6.41         3.32 
TCGA-L5-A4OP TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NU 
        7.17         8.71        25.12         3.95         3.02        83.24 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49W 
        0.07         0.16         0.07         0.33         0.07         0.07 
TCGA-LN-A49Y 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-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-S8-A6BW 
        0.07        17.62         5.16         3.78        14.01 

  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 
              4.90               3.32 
[1] "0.1 - 122.1 (4.9)" "0.0 - 83.2 (3.3)" 
[1] "hr=" "1.6"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED         4        2        2        1        13         9
  20Q GAIN WILD-TYPE       3        2        2        0        17         7
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED           7          6          3          1        1
  20Q GAIN WILD-TYPE         4          2          3          2        0
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   4                  3
  STAGE IA                  2                  2
  STAGE IB                  2                  2
  STAGE II                  1                  0
  STAGE IIA                13                 17
  STAGE IIB                 9                  7
  STAGE III                 7                  4
  STAGE IIIA                6                  2
  STAGE IIIB                3                  3
  STAGE IIIC                1                  2
  STAGE IV                  1                  0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  20Q GAIN MUTATED      14 11    26
  20Q GAIN WILD-TYPE     5 15    24
D37V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1               14                  5
  T2                  11                 15
  T3+T4               26                 24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  20Q GAIN MUTATED   24 22     5
  20Q GAIN WILD-TYPE 26 11     6
D37V5, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0                  24                 26
  N1                  22                 11
  N2+N3                5                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  20Q GAIN MUTATED   37   1  9
  20Q GAIN WILD-TYPE 38   0  6
D37V6, multiclass
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0                37                 38
  M1A                1                  0
  MX                 9                  6
[1] 3 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    8 53
  20Q GAIN WILD-TYPE  7 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      8   53
  20Q GAIN WILD-TYPE    7   37
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                8                  7
  MALE                 53                 37
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   16 43
  20Q GAIN WILD-TYPE 19 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     16   43
  20Q GAIN WILD-TYPE   19   23
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN               16                 19
  WHITE               43                 23
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    6  1
  21Q GAIN WILD-TYPE 61 30
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                 91 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                 30 
$`21Q GAIN MUTATED`
TCGA-IG-A3YB TCGA-IG-A8O2 TCGA-L5-A4OF TCGA-LN-A49L TCGA-LN-A49U TCGA-LN-A49V 
        2.63         0.46         3.68        10.45         0.07         0.10 
TCGA-S8-A6BV 
        8.78 

$`21Q GAIN WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09         0.85        20.78        20.12         0.03 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
        0.26         0.99         0.53        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.13         1.12       122.10        44.75        60.39        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
        3.68        41.52        42.77         6.21         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         4.31         8.94         3.52         3.35        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-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-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU 
        7.40         3.95         3.02        16.47        21.37        83.24 
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-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.13         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-A6BW TCGA-V5-A7RB 
        6.35        53.95         9.30         7.00        14.01         5.29 
TCGA-V5-A7RE 
        4.80 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.07               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             10.45             122.10 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              2.63               4.80 
[1] "0.1 - 10.4 (2.6)"  "0.0 - 122.1 (4.8)"
[1] "hr=" "1.4"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q GAIN MUTATED         0        0        0        0         4         1
  21Q GAIN WILD-TYPE       7        4        4        1        26        15
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           0          2          1          0        0
  21Q GAIN WILD-TYPE        11          6          5          3        1
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   0                  7
  STAGE IA                  0                  4
  STAGE IB                  0                  4
  STAGE II                  0                  1
  STAGE IIA                 4                 26
  STAGE IIB                 1                 15
  STAGE III                 0                 11
  STAGE IIIA                2                  6
  STAGE IIIB                1                  5
  STAGE IIIC                0                  3
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  21Q GAIN MUTATED       1  1     6
  21Q GAIN WILD-TYPE    18 25    44
D38V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1                1                 18
  T2                   1                 25
  T3+T4                6                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  21Q GAIN MUTATED    4  3     1
  21Q GAIN WILD-TYPE 46 30    10
D38V5, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                   4                 46
  N1                   3                 30
  N2+N3                1                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  21Q GAIN MUTATED    6   0  1
  21Q GAIN WILD-TYPE 69   1 14
D38V6, multiclass
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                 6                 69
  M1A                0                  1
  MX                 1                 14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    0  8
  21Q GAIN WILD-TYPE 15 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0    8
  21Q GAIN WILD-TYPE   15   82
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                0                 15
  MALE                  8                 82
[1] 2 2
[1] FALSE
D38V8, continuous
D38V9, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    5  3
  21Q GAIN WILD-TYPE 30 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      5    3
  21Q GAIN WILD-TYPE   30   63
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                5                 30
  WHITE                3                 63
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   12  3
  22Q GAIN WILD-TYPE 55 28
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                15                 83 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                 28 
$`22Q GAIN MUTATED`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OM 
       20.09         0.85        20.78         3.45         4.31         4.08 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.13         0.10         0.10         0.07         0.10         0.07 
TCGA-LN-A5U6 TCGA-Q9-A6FU TCGA-S8-A6BW 
        0.20         5.16        14.01 

$`22Q GAIN WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       33.27         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         1.12 
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        53.85         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M 
       41.52        42.77         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-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       16.47        21.37        83.24        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-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A5 
        0.10         0.07         0.10         0.07         0.07         0.10 
TCGA-LN-A4A8 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.07         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-V5-A7RB TCGA-V5-A7RE 
        9.30         7.00         8.78         5.29         4.80 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.07               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             20.78             122.10 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.85               5.06 
[1] "0.1 - 20.8 (0.8)"  "0.0 - 122.1 (5.1)"
[1] "hr=" "1.1"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         1        1        1        1         7         3
  22Q GAIN WILD-TYPE       6        3        3        0        23        13
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           2          2          1          0        0
  22Q GAIN WILD-TYPE         9          6          5          3        1
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   1                  6
  STAGE IA                  1                  3
  STAGE IB                  1                  3
  STAGE II                  1                  0
  STAGE IIA                 7                 23
  STAGE IIB                 3                 13
  STAGE III                 2                  9
  STAGE IIIA                2                  6
  STAGE IIIB                1                  5
  STAGE IIIC                0                  3
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  22Q GAIN MUTATED       2  7    10
  22Q GAIN WILD-TYPE    17 19    40
D39V4, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1                2                 17
  T2                   7                 19
  T3+T4               10                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  22Q GAIN MUTATED   15  3     1
  22Q GAIN WILD-TYPE 35 30    10
D39V5, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0                  15                 35
  N1                   3                 30
  N2+N3                1                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  22Q GAIN MUTATED   16   0  2
  22Q GAIN WILD-TYPE 59   1 13
D39V6, multiclass
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0                16                 59
  M1A                0                  1
  MX                 2                 13
[1] 3 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 17
  22Q GAIN WILD-TYPE 13 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2   17
  22Q GAIN WILD-TYPE   13   73
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                2                 13
  MALE                 17                 73
[1] 2 2
[1] FALSE
D39V8, continuous
D39V9, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED   11  8
  22Q GAIN WILD-TYPE 24 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     11    8
  22Q GAIN WILD-TYPE   24   58
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN               11                 24
  WHITE                8                 58
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED   14  5
  XQ GAIN WILD-TYPE 53 26
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               19                79 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                5                26 
$`XQ GAIN MUTATED`
TCGA-IG-A3QL TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A6QS TCGA-IG-A8O2 
       20.09         0.26         0.53        17.03         0.13         0.46 
TCGA-JY-A6F8 TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OQ TCGA-L5-A88Y TCGA-L5-A8NQ 
      122.10         4.31         8.78         1.38         0.36        21.37 
TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A4 
        0.07         0.13         0.10         0.10         0.13         0.10 
TCGA-S8-A6BV 
        8.78 

$`XQ GAIN WILD-TYPE`
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-A625 TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FB 
        0.99         0.79         0.36         1.12        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C 
       53.85         3.68        41.52        42.77         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-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       19.50         6.41         4.08        18.35         3.32         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-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-A8NJ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
        3.02        16.47        83.24        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-A7RE 
        4.80 

  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 
             0.46              5.06 
[1] "0.1 - 122.1 (0.5)" "0.0 - 83.2 (5.1)" 
[1] "hr=" "1"  
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         1        0        0        0         9         4
  XQ GAIN WILD-TYPE       6        4        4        1        21        12
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED           1          3          2          1        0
  XQ GAIN WILD-TYPE        10          5          4          2        1
D40V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  1                 6
  STAGE IA                 0                 4
  STAGE IB                 0                 4
  STAGE II                 0                 1
  STAGE IIA                9                21
  STAGE IIB                4                12
  STAGE III                1                10
  STAGE IIIA               3                 5
  STAGE IIIB               2                 4
  STAGE IIIC               1                 2
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  XQ GAIN MUTATED       3  4    15
  XQ GAIN WILD-TYPE    16 22    35
D40V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1               3                16
  T2                  4                22
  T3+T4              15                35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  XQ GAIN MUTATED   13  5     4
  XQ GAIN WILD-TYPE 37 28     7
D40V5, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0                 13                37
  N1                  5                28
  N2+N3               4                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  XQ GAIN MUTATED   17   0  5
  XQ GAIN WILD-TYPE 58   1 10
D40V6, multiclass
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0               17                58
  M1A               0                 1
  MX                5                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    0 22
  XQ GAIN WILD-TYPE 15 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   22
  XQ GAIN WILD-TYPE   15   68
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               0                15
  MALE                22                68
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   11 11
  XQ GAIN WILD-TYPE 24 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     11   11
  XQ GAIN WILD-TYPE   24   55
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN              11                24
  WHITE              11                55
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   13  7
  1P LOSS WILD-TYPE 54 24
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               20                78 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                7                24 
$`1P LOSS MUTATED`
TCGA-IG-A3I8 TCGA-IG-A4P3 TCGA-JY-A6FB TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE 
       33.27         0.03        60.39         0.30         8.94         3.52 
TCGA-L5-A4OG TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NJ 
        3.35         4.90        29.00         2.60         7.40        16.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ 
        0.20         1.18         8.02         7.59         5.06         6.35 
TCGA-S8-A6BW TCGA-V5-A7RE 
       14.01         4.80 

$`1P LOSS WILD-TYPE`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
       20.09         0.85        20.78         2.63        20.12         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-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        1.12         0.46       122.10        44.75        53.85         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J 
       41.52        42.77         6.21         3.16         3.45         4.31 
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-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW 
        3.32         7.17         1.38         3.16        30.74         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 
        7.43         6.94         8.71        25.12         0.36         3.95 
TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        3.02        21.37        83.24        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-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-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 
        0.07        17.62         5.16         3.78        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
       29.59        53.95         9.30         7.00         8.78         5.29 

  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 
            5.705             3.730 
[1] "0.0 - 60.4 (5.7)"  "0.1 - 122.1 (3.7)"
[1] "hr=" "1.1"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED         2        0        2        0         6         2
  1P LOSS WILD-TYPE       5        4        2        1        24        14
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED           3          0          1          0        1
  1P LOSS WILD-TYPE         8          8          5          3        0
D41V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  2                 5
  STAGE IA                 0                 4
  STAGE IB                 2                 2
  STAGE II                 0                 1
  STAGE IIA                6                24
  STAGE IIB                2                14
  STAGE III                3                 8
  STAGE IIIA               0                 8
  STAGE IIIB               1                 5
  STAGE IIIC               0                 3
  STAGE IV                 1                 0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  1P LOSS MUTATED       4  6     8
  1P LOSS WILD-TYPE    15 20    42
D41V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1               4                15
  T2                  6                20
  T3+T4               8                42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  1P LOSS MUTATED    9  7     2
  1P LOSS WILD-TYPE 41 26     9
D41V5, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0                  9                41
  N1                  7                26
  N2+N3               2                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  1P LOSS MUTATED   13   1  3
  1P LOSS WILD-TYPE 62   0 12
D41V6, multiclass
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               13                62
  M1A               1                 0
  MX                3                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    5 17
  1P LOSS WILD-TYPE 10 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      5   17
  1P LOSS WILD-TYPE   10   73
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               5                10
  MALE                17                73
[1] 2 2
[1] FALSE
D41V8, continuous
D41V9, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    4 17
  1P LOSS WILD-TYPE 31 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4   17
  1P LOSS WILD-TYPE   31   49
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN               4                31
  WHITE              17                49
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED    8  6
  1Q LOSS WILD-TYPE 59 25
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               14                84 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6                25 
$`1Q LOSS MUTATED`
TCGA-IG-A3I8 TCGA-IG-A4QS TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OT TCGA-L5-A88V 
       33.27         0.26         8.94         3.52         4.90         2.60 
TCGA-LN-A49O TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.33         0.20         1.18         8.02         7.59         5.06 
TCGA-R6-A6XQ TCGA-V5-A7RE 
        6.35         4.80 

$`1Q LOSS WILD-TYPE`
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-A625 TCGA-IG-A6QS 
        0.99         0.53        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 
        1.12         0.46       122.10        44.75        60.39        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
        3.68        41.52        42.77         6.21         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        0.30         4.31         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-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        30.74        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71        25.12         0.36         7.40         3.95         3.02 
TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       16.47        21.37        83.24        10.36         0.07        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
        0.16         0.07         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-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       17.62         5.16         3.78        14.70         7.04        29.59 
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 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.20              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            33.27            122.10 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            4.850             4.015 
[1] "0.2 - 33.3 (4.8)"  "0.0 - 122.1 (4.0)"
[1] "hr=" "2"  
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         0        0        1        0         3         1
  1Q LOSS WILD-TYPE       7        4        3        1        27        15
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED           1          0          2          0        1
  1Q LOSS WILD-TYPE        10          8          4          3        0
D42V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  0                 7
  STAGE IA                 0                 4
  STAGE IB                 1                 3
  STAGE II                 0                 1
  STAGE IIA                3                27
  STAGE IIB                1                15
  STAGE III                1                10
  STAGE IIIA               0                 8
  STAGE IIIB               2                 4
  STAGE IIIC               0                 3
  STAGE IV                 1                 0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  1Q LOSS MUTATED       1  2     7
  1Q LOSS WILD-TYPE    18 24    43
D42V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1               1                18
  T2                  2                24
  T3+T4               7                43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  1Q LOSS MUTATED    4  3     3
  1Q LOSS WILD-TYPE 46 30     8
D42V5, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0                  4                46
  N1                  3                30
  N2+N3               3                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  1Q LOSS MUTATED    6   1  2
  1Q LOSS WILD-TYPE 69   0 13
D42V6, multiclass
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0                6                69
  M1A               1                 0
  MX                2                13
[1] 3 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 11
  1Q LOSS WILD-TYPE 12 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3   11
  1Q LOSS WILD-TYPE   12   79
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               3                12
  MALE                11                79
[1] 2 2
[1] FALSE
D42V8, continuous
D42V9, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    3 10
  1Q LOSS WILD-TYPE 32 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3   10
  1Q LOSS WILD-TYPE   32   56
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN               3                32
  WHITE              10                56
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED    3  0
  2P LOSS WILD-TYPE 64 31
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                95 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                0                31 
$`2P LOSS MUTATED`
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-L5-A4OS 
        2.63        20.12        30.74 

$`2P LOSS WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27        20.09         0.85        20.78         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-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        1.12         0.46       122.10        44.75        60.39        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
        3.68        41.52        42.77         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-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38         3.16         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-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU 
        7.40         3.95         3.02        16.47        21.37        83.24 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         0.07        10.45         0.16         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-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-A7RE 
        7.00         8.78        14.01         5.29         4.80 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.63              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            30.74            122.10 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            20.12              4.08 
[1] "2.6 - 30.7 (20.1)" "0.0 - 122.1 (4.1)"
[1] "hr="     "2.7e+07"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED         0        0        0        0         2         1
  2P LOSS WILD-TYPE       7        4        4        1        28        15
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED           0          2          0          0        0
  2P LOSS WILD-TYPE        11          6          6          3        1
D43V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  0                 7
  STAGE IA                 0                 4
  STAGE IB                 0                 4
  STAGE II                 0                 1
  STAGE IIA                2                28
  STAGE IIB                1                15
  STAGE III                0                11
  STAGE IIIA               2                 6
  STAGE IIIB               0                 6
  STAGE IIIC               0                 3
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  2P LOSS MUTATED       0  3     2
  2P LOSS WILD-TYPE    19 23    48
D43V4, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1               0                19
  T2                  3                23
  T3+T4               2                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  2P LOSS MUTATED    2  3     0
  2P LOSS WILD-TYPE 48 30    11
D43V5, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0                  2                48
  N1                  3                30
  N2+N3               0                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  2P LOSS MUTATED    5   0  0
  2P LOSS WILD-TYPE 70   1 15
D43V6, multiclass
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0                5                70
  M1A               0                 1
  MX                0                15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    1  4
  2P LOSS WILD-TYPE 14 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1    4
  2P LOSS WILD-TYPE   14   86
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               1                14
  MALE                 4                86
[1] 2 2
[1] FALSE
D43V8, continuous
D43V9, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    2  3
  2P LOSS WILD-TYPE 33 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    3
  2P LOSS WILD-TYPE   33   63
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN               2                33
  WHITE               3                63
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    7  4
  2Q LOSS WILD-TYPE 60 27
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               11                87 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                4                27 
$`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-LN-A49L TCGA-LN-A49Y TCGA-LN-A4MQ 
        3.02        16.47        10.45         0.07         0.10 

$`2Q LOSS WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT 
       33.27        20.09         0.85        20.78         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         1.12         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        53.85         3.68        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M 
       42.77         6.21         3.16         3.45         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-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-A8NQ 
        2.60        25.12         0.36         7.40         3.95        21.37 
TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       83.24        10.36         0.07         0.16         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-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-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.07         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-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 
       14.01         5.29         4.80 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.03              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            30.74            122.10 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             2.63              4.80 
[1] "0.0 - 30.7 (2.6)"  "0.1 - 122.1 (4.8)"
[1] "hr=" "1.5"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED         1        0        1        0         4         2
  2Q LOSS WILD-TYPE       6        4        3        1        26        14
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED           3          2          0          0        0
  2Q LOSS WILD-TYPE         8          6          6          3        1
D44V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  1                 6
  STAGE IA                 0                 4
  STAGE IB                 1                 3
  STAGE II                 0                 1
  STAGE IIA                4                26
  STAGE IIB                2                14
  STAGE III                3                 8
  STAGE IIIA               2                 6
  STAGE IIIB               0                 6
  STAGE IIIC               0                 3
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  2Q LOSS MUTATED       1  5     7
  2Q LOSS WILD-TYPE    18 21    43
D44V4, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1               1                18
  T2                  5                21
  T3+T4               7                43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  2Q LOSS MUTATED    6  7     0
  2Q LOSS WILD-TYPE 44 26    11
D44V5, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0                  6                44
  N1                  7                26
  N2+N3               0                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  2Q LOSS MUTATED   13   0  0
  2Q LOSS WILD-TYPE 62   1 15
D44V6, multiclass
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0               13                62
  M1A               0                 1
  MX                0                15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    2 11
  2Q LOSS WILD-TYPE 13 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   11
  2Q LOSS WILD-TYPE   13   79
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               2                13
  MALE                11                79
[1] 2 2
[1] FALSE
D44V8, continuous
D44V9, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    5  8
  2Q LOSS WILD-TYPE 30 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    8
  2Q LOSS WILD-TYPE   30   58
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN               5                30
  WHITE               8                58
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED   39  9
  3P LOSS WILD-TYPE 28 22
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               48                50 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                22 
$`3P LOSS MUTATED`
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-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A6FD 
        0.26         0.53        17.03         0.79         0.13        53.85 
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-A8NJ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       16.47         0.07         0.07         0.33         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-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.07         0.10         0.07         0.20         1.18 
TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
       17.62         7.59         7.04         7.00         8.78        14.01 

$`3P LOSS WILD-TYPE`
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 
        0.03         0.99         0.36         1.12         0.46       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC 
       44.75        60.39         3.68        41.52        42.77         6.21 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OI 
        3.16         0.30         4.31         3.52         3.68         8.78 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        4.08        18.35         1.38         3.16        30.74         4.90 
TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
       29.00         8.71        25.12         0.36         3.95         3.02 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R 
       21.37        83.24        10.36        10.45         0.16         0.10 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A9 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.10         0.07         0.07         5.16         3.78         8.02 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        14.70        29.59         6.35        53.95         9.30 
TCGA-V5-A7RB TCGA-V5-A7RE 
        5.29         4.80 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.07              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            53.85            122.10 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            2.975             4.980 
[1] "0.1 - 53.9 (3.0)"  "0.0 - 122.1 (5.0)"
[1] "hr=" "1.5"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED         4        1        3        1        20         8
  3P LOSS WILD-TYPE       3        3        1        0        10         8
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED           6          6          1          1        0
  3P LOSS WILD-TYPE         5          2          5          2        1
D45V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  4                 3
  STAGE IA                 1                 3
  STAGE IB                 3                 1
  STAGE II                 1                 0
  STAGE IIA               20                10
  STAGE IIB                8                 8
  STAGE III                6                 5
  STAGE IIIA               6                 2
  STAGE IIIB               1                 5
  STAGE IIIC               1                 2
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  3P LOSS MUTATED       8 15    29
  3P LOSS WILD-TYPE    11 11    21
D45V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1               8                11
  T2                 15                11
  T3+T4              29                21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  3P LOSS MUTATED   31 18     3
  3P LOSS WILD-TYPE 19 15     8
D45V5, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0                 31                19
  N1                 18                15
  N2+N3               3                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  3P LOSS MUTATED   46   0  6
  3P LOSS WILD-TYPE 29   1  9
D45V6, multiclass
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0               46                29
  M1A               0                 1
  MX                6                 9
[1] 3 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   10 44
  3P LOSS WILD-TYPE  5 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     10   44
  3P LOSS WILD-TYPE    5   46
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              10                 5
  MALE                44                46
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   25 26
  3P LOSS WILD-TYPE 10 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     25   26
  3P LOSS WILD-TYPE   10   40
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN              25                10
  WHITE              26                40
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    9  3
  3Q LOSS WILD-TYPE 58 28
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               12                86 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                28 
$`3Q LOSS MUTATED`
TCGA-IG-A3YA TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OX TCGA-L5-A88Z 
       20.78         3.45        19.50         3.32         7.43         7.40 
TCGA-LN-A49K TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-RE-A7BO 
        0.07         0.07         0.10         0.20         1.18         7.00 

$`3Q LOSS WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09         0.85         2.63        20.12         0.03 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
        0.26         0.99         0.53        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
        0.13         1.12         0.46       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C 
       53.85         3.68        41.52        42.77         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-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
        8.78         6.41         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-A891 TCGA-L5-A893 
        8.71         2.60        25.12         0.36         3.95         3.02 
TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       16.47        21.37        83.24        10.36        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-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.07         0.10         0.13         0.07         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.07         0.07         0.10         0.07        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-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW 
       29.59         6.35        53.95         9.30         8.78        14.01 
TCGA-V5-A7RB TCGA-V5-A7RE 
        5.29         4.80 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.07              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            20.78            122.10 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            3.385             4.555 
[1] "0.1 - 20.8 (3.4)"  "0.0 - 122.1 (4.6)"
[1] "hr=" "1.1"
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         2        0        0        1         6         3
  3Q LOSS WILD-TYPE       5        4        4        0        24        13
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED           0          1          0          1        0
  3Q LOSS WILD-TYPE        11          7          6          2        1
D46V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  2                 5
  STAGE IA                 0                 4
  STAGE IB                 0                 4
  STAGE II                 1                 0
  STAGE IIA                6                24
  STAGE IIB                3                13
  STAGE III                0                11
  STAGE IIIA               1                 7
  STAGE IIIB               0                 6
  STAGE IIIC               1                 2
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  3Q LOSS MUTATED       4  5     5
  3Q LOSS WILD-TYPE    15 21    45
D46V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1               4                15
  T2                  5                21
  T3+T4               5                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  3Q LOSS MUTATED    9  4     1
  3Q LOSS WILD-TYPE 41 29    10
D46V5, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0                  9                41
  N1                  4                29
  N2+N3               1                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  3Q LOSS MUTATED   14   0  0
  3Q LOSS WILD-TYPE 61   1 15
D46V6, multiclass
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               14                61
  M1A               0                 1
  MX                0                15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2 12
  3Q LOSS WILD-TYPE 13 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2   12
  3Q LOSS WILD-TYPE   13   78
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               2                13
  MALE                12                78
[1] 2 2
[1] FALSE
D46V8, continuous
D46V9, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    7  7
  3Q LOSS WILD-TYPE 28 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      7    7
  3Q LOSS WILD-TYPE   28   59
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN               7                28
  WHITE               7                59
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   35 19
  4P LOSS WILD-TYPE 32 12
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               54                44 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               19                12 
$`4P LOSS MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09         0.85        20.78        20.12         0.03 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
        0.26         0.53         0.79         0.36         0.13         0.46 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE 
       44.75        60.39        42.77         3.16         8.94         3.52 
TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW 
        3.35         6.41         3.32         3.16         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49K 
        7.43         7.40         3.95        16.47        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-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE 
        7.04         6.35         9.30         7.00        14.01         4.80 

$`4P LOSS WILD-TYPE`
TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FD 
        2.63         0.99        17.03         1.12       122.10        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
        3.68        41.52         6.21         3.45         0.30         4.31 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
        3.68        19.50         8.78         4.08        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        1.38        30.74        29.00         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49O 
       25.12         0.36         3.02        21.37        83.24         0.33 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A9 
        0.13         0.10         0.07         0.10         0.10         0.07 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 
       17.62         5.16         3.78        14.70        29.59        53.95 
TCGA-S8-A6BV TCGA-V5-A7RB 
        8.78         5.29 

  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 
            3.435             5.225 
[1] "0.0 - 60.4 (3.4)"  "0.1 - 122.1 (5.2)"
[1] "hr=" "2"  
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED         3        1        3        1        16        10
  4P LOSS WILD-TYPE       4        3        1        0        14         6
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED           5          4          4          2        1
  4P LOSS WILD-TYPE         6          4          2          1        0
D47V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  3                 4
  STAGE IA                 1                 3
  STAGE IB                 3                 1
  STAGE II                 1                 0
  STAGE IIA               16                14
  STAGE IIB               10                 6
  STAGE III                5                 6
  STAGE IIIA               4                 4
  STAGE IIIB               4                 2
  STAGE IIIC               2                 1
  STAGE IV                 1                 0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  4P LOSS MUTATED       7 19    26
  4P LOSS WILD-TYPE    12  7    24
D47V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1               7                12
  T2                 19                 7
  T3+T4              26                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  4P LOSS MUTATED   26 19     7
  4P LOSS WILD-TYPE 24 14     4
D47V5, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0                 26                24
  N1                 19                14
  N2+N3               7                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  4P LOSS MUTATED   46   1  4
  4P LOSS WILD-TYPE 29   0 11
D47V6, multiclass
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0               46                29
  M1A               1                 0
  MX                4                11
[1] 3 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    8 51
  4P LOSS WILD-TYPE  7 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      8   51
  4P LOSS WILD-TYPE    7   39
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               8                 7
  MALE                51                39
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   25 32
  4P LOSS WILD-TYPE 10 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     25   32
  4P LOSS WILD-TYPE   10   34
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN              25                10
  WHITE              32                34
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   30 20
  4Q LOSS WILD-TYPE 37 11
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               50                48 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               20                11 
$`4Q LOSS MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A50L 
       33.27        20.09         0.85        20.78         0.26         0.53 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH 
        0.79         0.36         0.46        44.75        60.39        42.77 
TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OO 
        3.16         4.31         8.94         3.52         3.35         3.32 
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-A88Z TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K 
        7.40         3.95        16.47        83.24        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A3 
       10.45         0.16         0.10         0.07         0.07         0.07 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.10         0.10         0.20         1.18         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-RE-A7BO 
        5.06         7.04        29.59         6.35         9.30         7.00 
TCGA-S8-A6BW TCGA-V5-A7RE 
       14.01         4.80 

$`4Q LOSS WILD-TYPE`
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A6QS 
        2.63        20.12         0.03         0.99        17.03         0.13 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC 
        1.12       122.10        53.85         3.68        41.52         6.21 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.45         0.30         3.68        19.50         8.78         6.41 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A88T 
        4.08        18.35         7.17         1.38        29.00         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NQ TCGA-LN-A49N 
        2.60        25.12         0.36         3.02        21.37         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 

  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 
             4.98              3.68 
[1] "0.1 - 83.2 (5.0)"  "0.0 - 122.1 (3.7)"
[1] "hr=" "1.6"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED         2        1        4        1        13         9
  4Q LOSS WILD-TYPE       5        3        0        0        17         7
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED           5          3          4          2        1
  4Q LOSS WILD-TYPE         6          5          2          1        0
D48V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  2                 5
  STAGE IA                 1                 3
  STAGE IB                 4                 0
  STAGE II                 1                 0
  STAGE IIA               13                17
  STAGE IIB                9                 7
  STAGE III                5                 6
  STAGE IIIA               3                 5
  STAGE IIIB               4                 2
  STAGE IIIC               2                 1
  STAGE IV                 1                 0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  4Q LOSS MUTATED       6 16    25
  4Q LOSS WILD-TYPE    13 10    25
D48V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1               6                13
  T2                 16                10
  T3+T4              25                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  4Q LOSS MUTATED   24 16     7
  4Q LOSS WILD-TYPE 26 17     4
D48V5, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0                 24                26
  N1                 16                17
  N2+N3               7                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  4Q LOSS MUTATED   39   1  6
  4Q LOSS WILD-TYPE 36   0  9
D48V6, multiclass
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0               39                36
  M1A               1                 0
  MX                6                 9
[1] 3 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 47
  4Q LOSS WILD-TYPE  7 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8   47
  4Q LOSS WILD-TYPE    7   43
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               8                 7
  MALE                47                43
[1] 2 2
[1] FALSE
D48V8, continuous
D48V9, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   20 33
  4Q LOSS WILD-TYPE 15 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     20   33
  4Q LOSS WILD-TYPE   15   33
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN              20                15
  WHITE              33                33
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED   20  6
  5P LOSS WILD-TYPE 47 25
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               26                72 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                6                25 
$`5P LOSS MUTATED`
TCGA-IG-A3QL TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A6F8 
       20.09         0.26         0.53        17.03         0.46       122.10 
TCGA-JY-A6FB TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ 
       60.39         3.45         3.52         3.68         3.35         6.41 
TCGA-L5-A4OS TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-LN-A49K TCGA-LN-A49L 
       30.74         2.60         3.95         3.02         0.07        10.45 
TCGA-LN-A49V TCGA-LN-A4A8 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6XG TCGA-R6-A6XQ 
        0.10         0.07        17.62         5.16        29.59         6.35 
TCGA-R6-A6Y2 TCGA-S8-A6BV 
        9.30         8.78 

$`5P LOSS WILD-TYPE`
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-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA 
        0.99         0.79         0.36         0.13         1.12        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C 
       53.85         3.68        41.52        42.77         6.21         3.16 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM 
        0.30         4.31         8.94        19.50         8.78         4.08 
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-A88S TCGA-L5-A88T TCGA-L5-A88W 
       29.00         7.13         7.43         6.94         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ 
        0.36         7.40        16.47        21.37        83.24        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-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-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        7.04        53.95         7.00        14.01         5.29         4.80 

  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 
            4.555             4.195 
[1] "0.1 - 122.1 (4.6)" "0.0 - 83.2 (4.2)" 
[1] "hr=" "1.8"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P LOSS MUTATED         6        0        0        0         6         4
  5P LOSS WILD-TYPE       1        4        4        1        24        12
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           2          2          4          0        0
  5P LOSS WILD-TYPE         9          6          2          3        1
D49V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  6                 1
  STAGE IA                 0                 4
  STAGE IB                 0                 4
  STAGE II                 0                 1
  STAGE IIA                6                24
  STAGE IIB                4                12
  STAGE III                2                 9
  STAGE IIIA               2                 6
  STAGE IIIB               4                 2
  STAGE IIIC               0                 3
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  5P LOSS MUTATED       8  4    13
  5P LOSS WILD-TYPE    11 22    37
D49V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1               8                11
  T2                  4                22
  T3+T4              13                37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  5P LOSS MUTATED   13  8     4
  5P LOSS WILD-TYPE 37 25     7
D49V5, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0                 13                37
  N1                  8                25
  N2+N3               4                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  5P LOSS MUTATED   21   0  2
  5P LOSS WILD-TYPE 54   1 13
D49V6, multiclass
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               21                54
  M1A               0                 1
  MX                2                13
[1] 3 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 23
  5P LOSS WILD-TYPE 10 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5   23
  5P LOSS WILD-TYPE   10   67
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               5                10
  MALE                23                67
[1] 2 2
[1] FALSE
D49V8, continuous
D49V9, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    8 19
  5P LOSS WILD-TYPE 27 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      8   19
  5P LOSS WILD-TYPE   27   47
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN               8                27
  WHITE              19                47
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED   31 10
  5Q LOSS WILD-TYPE 36 21
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               41                57 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               10                21 
$`5Q LOSS MUTATED`
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
       20.09         2.63        20.12         0.03         0.26         0.53 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-L5-A43E TCGA-L5-A4OE 
        0.46       122.10        60.39        42.77         3.45         3.52 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR 
        3.68         3.35         6.41         4.08         7.17         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 
       30.74         4.90         7.13         2.60         0.36         3.95 
TCGA-L5-A893 TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49U TCGA-LN-A4A2 
        3.02         0.07        10.45         0.07         0.07         0.13 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.10         0.07         0.10         0.20        17.62         5.16 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-S8-A6BW 
       29.59         6.35         9.30         8.78        14.01 

$`5Q LOSS WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       33.27         0.85        20.78         0.99        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        0.36         0.13         1.12        44.75        53.85         3.68 
TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       41.52         6.21         3.16         0.30         4.31         8.94 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OU 
       19.50         8.78        18.35         3.32         1.38        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NJ 
        7.43         6.94         8.71        25.12         7.40        16.47 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R 
       21.37        83.24        10.36         0.16         0.33         0.10 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 
        0.13         0.10         0.07         0.10         0.07         0.07 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-Q9-A6FW 
        0.10         0.10         0.07         0.07         1.18         3.78 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 
        8.02         7.59         5.06        14.70         7.04        53.95 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
        7.00         5.29         4.80 

  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 
             3.68              5.06 
[1] "0.0 - 122.1 (3.7)" "0.1 - 83.2 (5.1)" 
[1] "hr=" "1.4"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED         6        3        1        0         9         8
  5Q LOSS WILD-TYPE       1        1        3        1        21         8
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED           3          4          4          0        1
  5Q LOSS WILD-TYPE         8          4          2          3        0
D50V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  6                 1
  STAGE IA                 3                 1
  STAGE IB                 1                 3
  STAGE II                 0                 1
  STAGE IIA                9                21
  STAGE IIB                8                 8
  STAGE III                3                 8
  STAGE IIIA               4                 4
  STAGE IIIB               4                 2
  STAGE IIIC               0                 3
  STAGE IV                 1                 0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  5Q LOSS MUTATED      11 12    18
  5Q LOSS WILD-TYPE     8 14    32
D50V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1              11                 8
  T2                 12                14
  T3+T4              18                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  5Q LOSS MUTATED   21 16     4
  5Q LOSS WILD-TYPE 29 17     7
D50V5, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0                 21                29
  N1                 16                17
  N2+N3               4                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  5Q LOSS MUTATED   31   1  6
  5Q LOSS WILD-TYPE 44   0  9
D50V6, multiclass
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               31                44
  M1A               1                 0
  MX                6                 9
[1] 3 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    8 36
  5Q LOSS WILD-TYPE  7 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      8   36
  5Q LOSS WILD-TYPE    7   54
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               8                 7
  MALE                36                54
[1] 2 2
[1] FALSE
D50V8, continuous
D50V9, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   14 28
  5Q LOSS WILD-TYPE 21 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     14   28
  5Q LOSS WILD-TYPE   21   38
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN              14                21
  WHITE              28                38
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   15  4
  6P LOSS WILD-TYPE 52 27
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               19                79 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                4                27 
$`6P LOSS MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A50L TCGA-JY-A6FB TCGA-L5-A43C TCGA-L5-A43J 
       33.27        20.09         0.53        60.39         3.16         4.31 
TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OR TCGA-L5-A88Y TCGA-L5-A8NJ TCGA-L5-A8NU 
        8.94         3.35         3.16         0.36        16.47        83.24 
TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A5U7 
        0.07         0.07         0.33         0.07         0.13         1.18 
TCGA-S8-A6BV 
        8.78 

$`6P LOSS WILD-TYPE`
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-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.99        17.03         0.79         0.36         0.13         1.12 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        0.46       122.10        44.75        53.85         3.68        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4OF 
       42.77         6.21         3.45         0.30         3.52         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-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-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-A8NQ TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
        3.95         3.02        21.37        10.36        10.45         0.16 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
        0.10         0.13         0.07         0.10         0.10         0.07 
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-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-A7RE 
        4.80 

  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 
             3.16              4.90 
[1] "0.1 - 83.2 (3.2)"  "0.0 - 122.1 (4.9)"
[1] "hr=" "1.7"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED         2        1        0        0         8         3
  6P LOSS WILD-TYPE       5        3        4        1        22        13
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED           2          2          0          0        0
  6P LOSS WILD-TYPE         9          6          6          3        1
D51V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  2                 5
  STAGE IA                 1                 3
  STAGE IB                 0                 4
  STAGE II                 0                 1
  STAGE IIA                8                22
  STAGE IIB                3                13
  STAGE III                2                 9
  STAGE IIIA               2                 6
  STAGE IIIB               0                 6
  STAGE IIIC               0                 3
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  6P LOSS MUTATED       4  4    12
  6P LOSS WILD-TYPE    15 22    38
D51V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1               4                15
  T2                  4                22
  T3+T4              12                38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  6P LOSS MUTATED   14  5     1
  6P LOSS WILD-TYPE 36 28    10
D51V5, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0                 14                36
  N1                  5                28
  N2+N3               1                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  6P LOSS MUTATED   15   0  5
  6P LOSS WILD-TYPE 60   1 10
D51V6, multiclass
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               15                60
  M1A               0                 1
  MX                5                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    3 18
  6P LOSS WILD-TYPE 12 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      3   18
  6P LOSS WILD-TYPE   12   72
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               3                12
  MALE                18                72
[1] 2 2
[1] FALSE
D51V8, continuous
D51V9, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    9 11
  6P LOSS WILD-TYPE 26 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      9   11
  6P LOSS WILD-TYPE   26   55
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN               9                26
  WHITE              11                55
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   17  3
  6Q LOSS WILD-TYPE 50 28
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               20                78 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                3                28 
$`6Q LOSS MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A8O2 TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43M 
       33.27        20.09         0.46        42.77         3.16         8.94 
TCGA-L5-A4OR TCGA-L5-A88Y TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49O 
        3.16         0.36        16.47        83.24         0.07         0.33 
TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-R6-A6XG 
        0.07         0.13         0.10         0.07         1.18        29.59 
TCGA-S8-A6BV TCGA-S8-A6BW 
        8.78        14.01 

$`6Q LOSS WILD-TYPE`
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-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 
        1.12       122.10        44.75        60.39        53.85         3.68 
TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE 
       41.52         6.21         3.45         0.30         4.31         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-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-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-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L7-A6VZ 
       25.12         7.40         3.95         3.02        21.37        10.36 
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-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
        0.10         0.10         0.07         0.07         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU 
        0.07         0.07         0.10         0.20        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-V5-A7RB TCGA-V5-A7RE 
        6.35        53.95         9.30         7.00         5.29         4.80 

  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 
            3.160             4.555 
[1] "0.1 - 83.2 (3.2)"  "0.0 - 122.1 (4.6)"
[1] "hr=" "2.8"
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED         0        1        1        0         9         2
  6Q LOSS WILD-TYPE       7        3        3        1        21        14
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           2          1          1          0        0
  6Q LOSS WILD-TYPE         9          7          5          3        1
D52V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  0                 7
  STAGE IA                 1                 3
  STAGE IB                 1                 3
  STAGE II                 0                 1
  STAGE IIA                9                21
  STAGE IIB                2                14
  STAGE III                2                 9
  STAGE IIIA               1                 7
  STAGE IIIB               1                 5
  STAGE IIIC               0                 3
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  6Q LOSS MUTATED       2  6    11
  6Q LOSS WILD-TYPE    17 20    39
D52V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1               2                17
  T2                  6                20
  T3+T4              11                39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  6Q LOSS MUTATED   13  4     2
  6Q LOSS WILD-TYPE 37 29     9
D52V5, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0                 13                37
  N1                  4                29
  N2+N3               2                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  6Q LOSS MUTATED   14   0  5
  6Q LOSS WILD-TYPE 61   1 10
D52V6, multiclass
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0               14                61
  M1A               0                 1
  MX                5                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    2 19
  6Q LOSS WILD-TYPE 13 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2   19
  6Q LOSS WILD-TYPE   13   71
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               2                13
  MALE                19                71
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    9 11
  6Q LOSS WILD-TYPE 26 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      9   11
  6Q LOSS WILD-TYPE   26   55
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN               9                26
  WHITE              11                55
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED    4  3
  7P LOSS WILD-TYPE 63 28
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                7                91 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3                28 
$`7P LOSS MUTATED`
TCGA-IG-A3Y9 TCGA-JY-A6FD TCGA-L5-A4OM TCGA-L5-A4OU TCGA-LN-A49L TCGA-LN-A4A8 
        0.85        53.85         4.08        29.00        10.45         0.07 
TCGA-Q9-A6FU 
        5.16 

$`7P LOSS WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09        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-A625 
        0.26         0.99         0.53        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
        0.13         1.12         0.46       122.10        44.75        60.39 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
        3.68        41.52        42.77         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-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ 
        3.95         3.02        16.47        21.37        83.24        10.36 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        0.07         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-A4A9 TCGA-LN-A4MQ 
        0.07         0.10         0.10         0.10         0.07         0.10 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.07         0.20         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-S8-A6BW TCGA-V5-A7RB 
       53.95         9.30         7.00         8.78        14.01         5.29 
TCGA-V5-A7RE 
        4.80 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.07              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            53.85            122.10 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             5.16              3.95 
[1] "0.1 - 53.9 (5.2)"  "0.0 - 122.1 (4.0)"
[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         0
  7P LOSS WILD-TYPE       7        3        4        1        26        16
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED           1          1          1          0        0
  7P LOSS WILD-TYPE        10          7          5          3        1
D53V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  0                 7
  STAGE IA                 1                 3
  STAGE IB                 0                 4
  STAGE II                 0                 1
  STAGE IIA                4                26
  STAGE IIB                0                16
  STAGE III                1                10
  STAGE IIIA               1                 7
  STAGE IIIB               1                 5
  STAGE IIIC               0                 3
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  7P LOSS MUTATED       1  2     5
  7P LOSS WILD-TYPE    18 24    45
D53V4, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1               1                18
  T2                  2                24
  T3+T4               5                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  7P LOSS MUTATED    6  1     1
  7P LOSS WILD-TYPE 44 32    10
D53V5, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0                  6                44
  N1                  1                32
  N2+N3               1                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  7P LOSS MUTATED    7   0  0
  7P LOSS WILD-TYPE 68   1 15
D53V6, multiclass
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0                7                68
  M1A               0                 1
  MX                0                15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    3  5
  7P LOSS WILD-TYPE 12 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3    5
  7P LOSS WILD-TYPE   12   85
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               3                12
  MALE                 5                85
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    4  4
  7P LOSS WILD-TYPE 31 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      4    4
  7P LOSS WILD-TYPE   31   62
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN               4                31
  WHITE               4                62
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED    6  4
  7Q LOSS WILD-TYPE 61 27
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               10                88 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4                27 
$`7Q LOSS MUTATED`
TCGA-IG-A3Y9 TCGA-IG-A5B8 TCGA-JY-A6FD TCGA-L5-A4OU TCGA-LN-A49L TCGA-LN-A49W 
        0.85         0.79        53.85        29.00        10.45         0.07 
TCGA-LN-A49X TCGA-LN-A4A3 TCGA-M9-A5M8 TCGA-R6-A6KZ 
        0.10         0.07        17.62         5.06 

$`7Q LOSS WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09        20.78         2.63        20.12         0.03 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
        0.26         0.99         0.53        17.03         0.36         0.13 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE 
        1.12         0.46       122.10        44.75        60.39         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       41.52        42.77         6.21         3.16         3.45         0.30 
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-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
        8.78         6.41         4.08        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-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ 
        3.95         3.02        16.47        21.37        83.24        10.36 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        0.07         0.16         0.07         0.33         0.10         0.13 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.07         0.10         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-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
        1.18         5.16         3.78         8.02         7.59        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-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        8.78        14.01         5.29         4.80 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.07              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            53.85            122.10 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            2.955             4.195 
[1] "0.1 - 53.9 (3.0)"  "0.0 - 122.1 (4.2)"
[1] "hr=" "1.3"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q LOSS MUTATED         0        0        1        0         5         0
  7Q LOSS WILD-TYPE       7        4        3        1        25        16
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED           3          1          0          0        0
  7Q LOSS WILD-TYPE         8          7          6          3        1
D54V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  0                 7
  STAGE IA                 0                 4
  STAGE IB                 1                 3
  STAGE II                 0                 1
  STAGE IIA                5                25
  STAGE IIB                0                16
  STAGE III                3                 8
  STAGE IIIA               1                 7
  STAGE IIIB               0                 6
  STAGE IIIC               0                 3
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  7Q LOSS MUTATED       0  1     9
  7Q LOSS WILD-TYPE    19 25    41
D54V4, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1               0                19
  T2                  1                25
  T3+T4               9                41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  7Q LOSS MUTATED    7  3     0
  7Q LOSS WILD-TYPE 43 30    11
D54V5, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0                  7                43
  N1                  3                30
  N2+N3               0                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  7Q LOSS MUTATED   10   0  0
  7Q LOSS WILD-TYPE 65   1 15
D54V6, multiclass
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0               10                65
  M1A               0                 1
  MX                0                15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    1 10
  7Q LOSS WILD-TYPE 14 80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   10
  7Q LOSS WILD-TYPE   14   80
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               1                14
  MALE                10                80
[1] 2 2
[1] FALSE
D54V8, continuous
D54V9, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    6  4
  7Q LOSS WILD-TYPE 29 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      6    4
  7Q LOSS WILD-TYPE   29   62
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN               6                29
  WHITE               4                62
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   22  8
  8P LOSS WILD-TYPE 45 23
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               30                68 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8                23 
$`8P LOSS MUTATED`
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
        0.85         2.63        20.12         0.26         0.53         0.79 
TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FB TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH 
        0.13        44.75        60.39         3.52         3.68        19.50 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A891 TCGA-LN-A49M 
        6.41         3.32         7.43         7.40         3.95         0.16 
TCGA-LN-A49N TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.07         0.07         0.13         0.10         0.10         0.07 
TCGA-LN-A5U6 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-S8-A6BW TCGA-V5-A7RB 
        0.20         5.16         3.78         8.02        14.01         5.29 

$`8P LOSS WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D 
       33.27        20.09        20.78         0.03         0.99        17.03 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE 
        0.36         1.12         0.46       122.10        53.85         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       41.52        42.77         6.21         3.16         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON 
        4.31         8.94         3.35         8.78         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-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.13         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K 
        3.02        16.47        21.37        83.24        10.36         0.07 
TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       10.45         0.33         0.10         0.13         0.07         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.07         0.10         0.07         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.07         1.18        17.62         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-A6BV TCGA-V5-A7RE 
        8.78         4.80 

  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 
            3.420             5.635 
[1] "0.1 - 60.4 (3.4)"  "0.0 - 122.1 (5.6)"
[1] "hr=" "1.2"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED         3        0        2        0         8         6
  8P LOSS WILD-TYPE       4        4        2        1        22        10
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED           1          4          4          1        0
  8P LOSS WILD-TYPE        10          4          2          2        1
D55V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  3                 4
  STAGE IA                 0                 4
  STAGE IB                 2                 2
  STAGE II                 0                 1
  STAGE IIA                8                22
  STAGE IIB                6                10
  STAGE III                1                10
  STAGE IIIA               4                 4
  STAGE IIIB               4                 2
  STAGE IIIC               1                 2
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  8P LOSS MUTATED       6 10    15
  8P LOSS WILD-TYPE    13 16    35
D55V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1               6                13
  T2                 10                16
  T3+T4              15                35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  8P LOSS MUTATED   13 13     5
  8P LOSS WILD-TYPE 37 20     6
D55V5, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0                 13                37
  N1                 13                20
  N2+N3               5                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  8P LOSS MUTATED   27   0  2
  8P LOSS WILD-TYPE 48   1 13
D55V6, multiclass
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0               27                48
  M1A               0                 1
  MX                2                13
[1] 3 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    3 29
  8P LOSS WILD-TYPE 12 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3   29
  8P LOSS WILD-TYPE   12   61
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               3                12
  MALE                29                61
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   12 19
  8P LOSS WILD-TYPE 23 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     12   19
  8P LOSS WILD-TYPE   23   47
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN              12                23
  WHITE              19                47
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    8  1
  8Q LOSS WILD-TYPE 59 30
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9                89 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                30 
$`8Q LOSS MUTATED`
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A891 
       44.75        60.39         3.68        19.50         6.41         3.95 
TCGA-LN-A49N TCGA-LN-A49Y TCGA-LN-A4MR 
        0.07         0.07         0.07 

$`8Q LOSS WILD-TYPE`
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-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-JY-A6F8 TCGA-JY-A6FD 
        0.36         0.13         1.12         0.46       122.10        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
        3.68        41.52        42.77         6.21         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI 
        0.30         4.31         8.94         3.52         3.35         8.78 
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-A893 
        8.71         2.60        25.12         0.36         7.40         3.02 
TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       16.47        21.37        83.24        10.36         0.07        10.45 
TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
        0.16         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-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.07         0.07         0.10         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-A7RE 
        7.00         8.78        14.01         5.29         4.80 

  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 
             3.95              4.31 
[1] "0.1 - 60.4 (4.0)"  "0.0 - 122.1 (4.3)"
[1] "hr=" "3.7"
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         3        0        0        0         3         3
  8Q LOSS WILD-TYPE       4        4        4        1        27        13
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED           0          0          0          0        0
  8Q LOSS WILD-TYPE        11          8          6          3        1
D56V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  3                 4
  STAGE IA                 0                 4
  STAGE IB                 0                 4
  STAGE II                 0                 1
  STAGE IIA                3                27
  STAGE IIB                3                13
  STAGE III                0                11
  STAGE IIIA               0                 8
  STAGE IIIB               0                 6
  STAGE IIIC               0                 3
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  8Q LOSS MUTATED       4  4     2
  8Q LOSS WILD-TYPE    15 22    48
D56V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1               4                15
  T2                  4                22
  T3+T4               2                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  8Q LOSS MUTATED    6  4     0
  8Q LOSS WILD-TYPE 44 29    11
D56V5, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0                  6                44
  N1                  4                29
  N2+N3               0                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  8Q LOSS MUTATED    9   0  0
  8Q LOSS WILD-TYPE 66   1 15
D56V6, multiclass
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0                9                66
  M1A               0                 1
  MX                0                15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    1  9
  8Q LOSS WILD-TYPE 14 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    9
  8Q LOSS WILD-TYPE   14   81
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               1                14
  MALE                 9                81
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    5  5
  8Q LOSS WILD-TYPE 30 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      5    5
  8Q LOSS WILD-TYPE   30   61
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN               5                30
  WHITE               5                61
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   39 13
  9P LOSS WILD-TYPE 28 18
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               52                46 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               13                18 
$`9P LOSS MUTATED`
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A6QS 
       20.12         0.03         0.26         0.53         0.79         0.13 
TCGA-IG-A8O2 TCGA-JY-A6FB TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH 
        0.46        60.39         3.16         8.94         3.68        19.50 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OW 
        4.08        18.35         3.32         7.17        30.74         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NU 
        7.43         6.94         2.60         3.95        16.47        83.24 
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-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
        0.07         0.10         0.07         0.13         0.07         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.07         0.10         0.07         0.20         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ 
       17.62         5.16         5.06        14.70        29.59         6.35 
TCGA-R6-A6Y2 TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        9.30         8.78         5.29         4.80 

$`9P LOSS WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT 
       33.27        20.09         0.85        20.78         2.63         0.99 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
       17.03         0.36         1.12       122.10        44.75        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
        3.68        41.52        42.77         6.21         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OQ 
        4.31         3.52         3.35         8.78         6.41         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y 
        3.16         4.90        29.00         8.71        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O 
        7.40         3.02        21.37        10.36         0.07         0.33 
TCGA-LN-A49V TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.10         0.10         0.07         3.78         8.02         7.59 
TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BW 
        7.04        53.95         7.00        14.01 

  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 
             3.50              6.31 
[1] "0.0 - 83.2 (3.5)"  "0.1 - 122.1 (6.3)"
[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        17         9
  9P LOSS WILD-TYPE       5        2        1        0        13         7
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED           7          3          3          1        0
  9P LOSS WILD-TYPE         4          5          3          2        1
D57V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  2                 5
  STAGE IA                 2                 2
  STAGE IB                 3                 1
  STAGE II                 1                 0
  STAGE IIA               17                13
  STAGE IIB                9                 7
  STAGE III                7                 4
  STAGE IIIA               3                 5
  STAGE IIIB               3                 3
  STAGE IIIC               1                 2
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  9P LOSS MUTATED       8 18    25
  9P LOSS WILD-TYPE    11  8    25
D57V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1               8                11
  T2                 18                 8
  T3+T4              25                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  9P LOSS MUTATED   25 21     5
  9P LOSS WILD-TYPE 25 12     6
D57V5, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0                 25                25
  N1                 21                12
  N2+N3               5                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  9P LOSS MUTATED   42   0  6
  9P LOSS WILD-TYPE 33   1  9
D57V6, multiclass
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0               42                33
  M1A               0                 1
  MX                6                 9
[1] 3 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    6 51
  9P LOSS WILD-TYPE  9 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6   51
  9P LOSS WILD-TYPE    9   39
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               6                 9
  MALE                51                39
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   25 28
  9P LOSS WILD-TYPE 10 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     25   28
  9P LOSS WILD-TYPE   10   38
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN              25                10
  WHITE              28                38
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   20 11
  9Q LOSS WILD-TYPE 47 20
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               31                67 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11                20 
$`9Q LOSS MUTATED`
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 
        0.85        20.78        20.12         0.03         0.26         0.79 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OS 
        0.13         0.46         8.94         3.68         4.08        30.74 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M 
        7.13         6.94         2.60        83.24        10.45         0.16 
TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A6 
        0.07         0.10         0.13         0.07         0.07         0.10 
TCGA-LN-A5U6 TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-V5-A7RB 
        0.20         5.06        29.59         6.35         9.30         5.29 
TCGA-V5-A7RE 
        4.80 

$`9Q LOSS WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       33.27        20.09         2.63         0.99         0.53        17.03 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        0.36         1.12       122.10        44.75        60.39        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
        3.68        41.52        42.77         6.21         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        0.30         4.31         3.52         3.35        19.50         8.78 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
        6.41        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y 
        4.90        29.00         7.43         8.71        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L7-A6VZ 
        7.40         3.95         3.02        16.47        21.37        10.36 
TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.07         0.33         0.07         0.10         0.07         0.10 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.13         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-A6DN 
        0.07         1.18        17.62         5.16         3.78         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BV 
        7.59        14.70         7.04        53.95         7.00         8.78 
TCGA-S8-A6BW 
       14.01 

  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 
             3.68              4.90 
[1] "0.0 - 83.2 (3.7)"  "0.1 - 122.1 (4.9)"
[1] "hr=" "1.6"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED         0        1        3        1         9         7
  9Q LOSS WILD-TYPE       7        3        1        0        21         9
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           4          3          2          0        0
  9Q LOSS WILD-TYPE         7          5          4          3        1
D58V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  0                 7
  STAGE IA                 1                 3
  STAGE IB                 3                 1
  STAGE II                 1                 0
  STAGE IIA                9                21
  STAGE IIB                7                 9
  STAGE III                4                 7
  STAGE IIIA               3                 5
  STAGE IIIB               2                 4
  STAGE IIIC               0                 3
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  9Q LOSS MUTATED       4 13    15
  9Q LOSS WILD-TYPE    15 13    35
D58V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1               4                15
  T2                 13                13
  T3+T4              15                35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  9Q LOSS MUTATED   16 13     3
  9Q LOSS WILD-TYPE 34 20     8
D58V5, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0                 16                34
  N1                 13                20
  N2+N3               3                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  9Q LOSS MUTATED   26   0  4
  9Q LOSS WILD-TYPE 49   1 11
D58V6, multiclass
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0               26                49
  M1A               0                 1
  MX                4                11
[1] 3 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    4 32
  9Q LOSS WILD-TYPE 11 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4   32
  9Q LOSS WILD-TYPE   11   58
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               4                11
  MALE                32                58
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   15 18
  9Q LOSS WILD-TYPE 20 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     15   18
  9Q LOSS WILD-TYPE   20   48
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN              15                20
  WHITE              18                48
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   15  7
  10P LOSS WILD-TYPE 52 24
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                22                 76 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 7                 24 
$`10P LOSS MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A43H TCGA-L5-A43J 
       33.27         0.85         0.53         0.79         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-A8NU TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       83.24         0.16         0.33         0.07         0.10         0.07 
TCGA-LN-A5U7 TCGA-Q9-A6FW TCGA-R6-A6Y0 TCGA-V5-A7RE 
        1.18         3.78        53.95         4.80 

$`10P LOSS WILD-TYPE`
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       20.09        20.78         2.63        20.12         0.03         0.26 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.99        17.03         0.36         0.13         1.12         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        53.85         3.68        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH 
       42.77         6.21         3.16         3.45         3.68        19.50 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
        8.78         6.41         4.08        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        3.16        30.74        29.00         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-A8NJ TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
       16.47        21.37        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-A6Y2 
        5.06        14.70         7.04        29.59         6.35         9.30 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        7.00         8.78        14.01         5.29 

  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 
             3.335              5.750 
[1] "0.1 - 83.2 (3.3)"  "0.0 - 122.1 (5.8)"
[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         9         2
  10P LOSS WILD-TYPE       6        4        2        1        21        14
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           2          2          2          1        1
  10P LOSS WILD-TYPE         9          6          4          2        0
D59V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   1                  6
  STAGE IA                  0                  4
  STAGE IB                  2                  2
  STAGE II                  0                  1
  STAGE IIA                 9                 21
  STAGE IIB                 2                 14
  STAGE III                 2                  9
  STAGE IIIA                2                  6
  STAGE IIIB                2                  4
  STAGE IIIC                1                  2
  STAGE IV                  1                  0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  10P LOSS MUTATED       2  8    13
  10P LOSS WILD-TYPE    17 18    37
D59V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1                2                 17
  T2                   8                 18
  T3+T4               13                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  10P LOSS MUTATED   14  5     4
  10P LOSS WILD-TYPE 36 28     7
D59V5, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                  14                 36
  N1                   5                 28
  N2+N3                4                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  10P LOSS MUTATED   19   1  2
  10P LOSS WILD-TYPE 56   0 13
D59V6, multiclass
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0                19                 56
  M1A                1                  0
  MX                 2                 13
[1] 3 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    4 20
  10P LOSS WILD-TYPE 11 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4   20
  10P LOSS WILD-TYPE   11   70
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                4                 11
  MALE                 20                 70
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    9 13
  10P LOSS WILD-TYPE 26 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      9   13
  10P LOSS WILD-TYPE   26   53
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                9                 26
  WHITE               13                 53
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   20  6
  10Q LOSS WILD-TYPE 47 25
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                26                 72 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                 25 
$`10Q LOSS MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A50L TCGA-L5-A43C TCGA-L5-A43H 
       33.27         0.85         2.63         0.53         3.16         0.30 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NU 
        3.52         3.35         3.32         4.90         7.13        83.24 
TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.16         0.10         0.07         0.13         0.10         0.10 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-Q9-A6FU 
        0.07         0.10         0.07         0.20         1.18         5.16 
TCGA-R6-A6Y0 TCGA-V5-A7RE 
       53.95         4.80 

$`10Q LOSS WILD-TYPE`
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.09        20.78        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         1.12         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        53.85         3.68        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF 
       42.77         6.21         3.45         4.31         8.94         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-A8NJ TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        3.02        16.47        21.37        10.36         0.07        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
        0.07         0.33         0.13         0.07         0.10         0.07 
TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.10         0.07         0.10         0.07        17.62         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 

  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 
             1.015              6.675 
[1] "0.1 - 83.2 (1.0)"  "0.0 - 122.1 (6.7)"
[1] "hr=" "1.1"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED         1        0        1        1        11         2
  10Q LOSS WILD-TYPE       6        4        3        0        19        14
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           4          3          2          1        1
  10Q LOSS WILD-TYPE         7          5          4          2        0
D60V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   1                  6
  STAGE IA                  0                  4
  STAGE IB                  1                  3
  STAGE II                  1                  0
  STAGE IIA                11                 19
  STAGE IIB                 2                 14
  STAGE III                 4                  7
  STAGE IIIA                3                  5
  STAGE IIIB                2                  4
  STAGE IIIC                1                  2
  STAGE IV                  1                  0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  10Q LOSS MUTATED       2 11    14
  10Q LOSS WILD-TYPE    17 15    36
D60V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1                2                 17
  T2                  11                 15
  T3+T4               14                 36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  10Q LOSS MUTATED   15  9     3
  10Q LOSS WILD-TYPE 35 24     8
D60V5, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                  15                 35
  N1                   9                 24
  N2+N3                3                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  10Q LOSS MUTATED   25   1  0
  10Q LOSS WILD-TYPE 50   0 15
D60V6, multiclass
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                25                 50
  M1A                1                  0
  MX                 0                 15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    4 25
  10Q LOSS WILD-TYPE 11 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4   25
  10Q LOSS WILD-TYPE   11   65
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                4                 11
  MALE                 25                 65
[1] 2 2
[1] FALSE
D60V8, continuous
D60V9, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   15 13
  10Q LOSS WILD-TYPE 20 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     15   13
  10Q LOSS WILD-TYPE   20   53
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN               15                 20
  WHITE               13                 53
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   22  7
  11P LOSS WILD-TYPE 45 24
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                29                 69 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                 24 
$`11P LOSS MUTATED`
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OG TCGA-L5-A4OO 
        0.85         2.63         3.16         0.30         3.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 
        7.17         3.16         6.94         2.60         0.36         3.02 
TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       16.47        10.36         0.07        10.45         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
        0.33         0.10         0.07         0.13         0.07         0.10 
TCGA-LN-A5U6 TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-V5-A7RE 
        0.20         5.06        29.59         6.35         4.80 

$`11P LOSS WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27        20.09        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-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        1.12         0.46       122.10        44.75        60.39        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J 
        3.68        41.52        42.77         6.21         3.45         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        8.94         3.52         3.68        19.50         8.78         6.41 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        4.08        18.35         1.38        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.13         7.43         8.71        25.12         7.40         3.95 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       21.37        83.24         0.13         0.07         0.10         0.10 
TCGA-LN-A49Y 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-A6DN 
        0.07         1.18        17.62         5.16         3.78         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO 
        7.59        14.70         7.04        53.95         9.30         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        8.78        14.01         5.29 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.07               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             29.59             122.10 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              2.63               6.41 
[1] "0.1 - 29.6 (2.6)"  "0.0 - 122.1 (6.4)"
[1] "hr=" "1.6"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P LOSS MUTATED         2        2        2        1         6         2
  11P LOSS WILD-TYPE       5        2        2        0        24        14
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED           7          2          0          2        0
  11P LOSS WILD-TYPE         4          6          6          1        1
D61V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   2                  5
  STAGE IA                  2                  2
  STAGE IB                  2                  2
  STAGE II                  1                  0
  STAGE IIA                 6                 24
  STAGE IIB                 2                 14
  STAGE III                 7                  4
  STAGE IIIA                2                  6
  STAGE IIIB                0                  6
  STAGE IIIC                2                  1
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  11P LOSS MUTATED       6  5    16
  11P LOSS WILD-TYPE    13 21    34
D61V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1                6                 13
  T2                   5                 21
  T3+T4               16                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  11P LOSS MUTATED   15 10     2
  11P LOSS WILD-TYPE 35 23     9
D61V5, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                  15                 35
  N1                  10                 23
  N2+N3                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  11P LOSS MUTATED   21   0  6
  11P LOSS WILD-TYPE 54   1  9
D61V6, multiclass
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                21                 54
  M1A                0                  1
  MX                 6                  9
[1] 3 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    3 28
  11P LOSS WILD-TYPE 12 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3   28
  11P LOSS WILD-TYPE   12   62
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                3                 12
  MALE                 28                 62
[1] 2 2
[1] FALSE
D61V8, continuous
D61V9, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   13 18
  11P LOSS WILD-TYPE 22 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     13   18
  11P LOSS WILD-TYPE   22   48
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN               13                 22
  WHITE               18                 48
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   24  6
  11Q LOSS WILD-TYPE 43 25
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                30                 68 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 6                 25 
$`11Q LOSS MUTATED`
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A6QS TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43H 
       20.12         0.03         0.13        42.77         3.16         0.30 
TCGA-L5-A4OG TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A88S 
        3.35         4.08         3.32         7.17         3.16         6.94 
TCGA-L5-A88V TCGA-L5-A893 TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
        2.60         3.02        10.36        10.45         0.16         0.07 
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 

$`11Q LOSS WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS 
       33.27        20.09         0.85        20.78         2.63         0.26 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP 
        0.99         0.53        17.03         0.79         0.36         1.12 
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        53.85         3.68 
TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       41.52         6.21         3.45         4.31         8.94         3.52 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ 
        3.68        19.50         8.78         6.41        18.35         1.38 
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-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NQ 
       25.12         0.36         7.40         3.95        16.47        21.37 
TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X 
       83.24         0.07         0.33         0.13         0.07         0.10 
TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A9 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-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       17.62         5.16         3.78         8.02         7.59        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW 
        7.04        29.59        53.95         9.30         7.00        14.01 
TCGA-V5-A7RB TCGA-V5-A7RE 
        5.29         4.80 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.03               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             42.77             122.10 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              2.81               6.31 
[1] "0.0 - 42.8 (2.8)"  "0.1 - 122.1 (6.3)"
[1] "hr=" "1.1"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED         2        3        1        1         7         5
  11Q LOSS WILD-TYPE       5        1        3        0        23        11
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED           6          2          0          2        0
  11Q LOSS WILD-TYPE         5          6          6          1        1
D62V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   2                  5
  STAGE IA                  3                  1
  STAGE IB                  1                  3
  STAGE II                  1                  0
  STAGE IIA                 7                 23
  STAGE IIB                 5                 11
  STAGE III                 6                  5
  STAGE IIIA                2                  6
  STAGE IIIB                0                  6
  STAGE IIIC                2                  1
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  11Q LOSS MUTATED       5 10    14
  11Q LOSS WILD-TYPE    14 16    36
D62V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1                5                 14
  T2                  10                 16
  T3+T4               14                 36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  11Q LOSS MUTATED   14 13     2
  11Q LOSS WILD-TYPE 36 20     9
D62V5, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                  14                 36
  N1                  13                 20
  N2+N3                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  11Q LOSS MUTATED   22   0  6
  11Q LOSS WILD-TYPE 53   1  9
D62V6, multiclass
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                22                 53
  M1A                0                  1
  MX                 6                  9
[1] 3 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    4 28
  11Q LOSS WILD-TYPE 11 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      4   28
  11Q LOSS WILD-TYPE   11   62
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                4                 11
  MALE                 28                 62
[1] 2 2
[1] FALSE
D62V8, continuous
D62V9, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   14 18
  11Q LOSS WILD-TYPE 21 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     14   18
  11Q LOSS WILD-TYPE   21   48
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN               14                 21
  WHITE               18                 48
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED   12  5
  12P LOSS WILD-TYPE 55 26
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                17                 81 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                 26 
$`12P LOSS MUTATED`
TCGA-IG-A3I8 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-JY-A6FH TCGA-L5-A43E TCGA-L5-A43M 
       33.27         0.26         0.79        42.77         3.45         8.94 
TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A891 
       19.50         7.17         1.38        30.74         7.13         3.95 
TCGA-L5-A893 TCGA-LN-A49M TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-S8-A6BV 
        3.02         0.16         3.78         5.06         8.78 

$`12P LOSS WILD-TYPE`
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-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.99         0.53        17.03         0.36         0.13         1.12 
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        53.85         3.68 
TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE 
       41.52         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-A8NJ 
        8.71         2.60        25.12         0.36         7.40        16.47 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
       21.37        83.24        10.36         0.07        10.45         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-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
        1.18        17.62         5.16         8.02         7.59        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-A7RE 
       14.01         5.29         4.80 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.16               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             42.77             122.10 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              5.06               4.08 
[1] "0.2 - 42.8 (5.1)"  "0.0 - 122.1 (4.1)"
[1] "hr=" "1.2"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED         3        1        1        0         3         3
  12P LOSS WILD-TYPE       4        3        3        1        27        13
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED           1          2          2          0        0
  12P LOSS WILD-TYPE        10          6          4          3        1
D63V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   3                  4
  STAGE IA                  1                  3
  STAGE IB                  1                  3
  STAGE II                  0                  1
  STAGE IIA                 3                 27
  STAGE IIB                 3                 13
  STAGE III                 1                 10
  STAGE IIIA                2                  6
  STAGE IIIB                2                  4
  STAGE IIIC                0                  3
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  12P LOSS MUTATED       4  6     8
  12P LOSS WILD-TYPE    15 20    42
D63V4, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1                4                 15
  T2                   6                 20
  T3+T4                8                 42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  12P LOSS MUTATED    8  6     4
  12P LOSS WILD-TYPE 42 27     7
D63V5, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0                   8                 42
  N1                   6                 27
  N2+N3                4                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  12P LOSS MUTATED   14   0  4
  12P LOSS WILD-TYPE 61   1 11
D63V6, multiclass
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0                14                 61
  M1A                0                  1
  MX                 4                 11
[1] 3 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 13
  12P LOSS WILD-TYPE  9 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      6   13
  12P LOSS WILD-TYPE    9   77
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                6                  9
  MALE                 13                 77
[1] 2 2
[1] FALSE
D63V8, continuous
D63V9, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    3 14
  12P LOSS WILD-TYPE 32 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3   14
  12P LOSS WILD-TYPE   32   52
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                3                 32
  WHITE               14                 52
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED   10  4
  12Q LOSS WILD-TYPE 57 27
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                14                 84 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 27 
$`12Q LOSS MUTATED`
TCGA-IG-A3I8 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-JY-A6FH TCGA-L5-A43E TCGA-L5-A43M 
       33.27         0.26         0.79        42.77         3.45         8.94 
TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A893 TCGA-Q9-A6FW 
       19.50         7.17        30.74         7.13         3.02         3.78 
TCGA-R6-A6KZ TCGA-S8-A6BV 
        5.06         8.78 

$`12Q LOSS WILD-TYPE`
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-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.99         0.53        17.03         0.36         0.13         1.12 
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        53.85         3.68 
TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE 
       41.52         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-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        3.32         1.38         3.16         4.90        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-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K 
        3.95        16.47        21.37        83.24        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 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.26               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             42.77             122.10 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             7.150              3.815 
[1] "0.3 - 42.8 (7.2)"  "0.0 - 122.1 (3.8)"
[1] "hr=" "1.4"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q LOSS MUTATED         3        1        1        0         2         3
  12Q LOSS WILD-TYPE       4        3        3        1        28        13
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED           0          1          2          0        0
  12Q LOSS WILD-TYPE        11          7          4          3        1
D64V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   3                  4
  STAGE IA                  1                  3
  STAGE IB                  1                  3
  STAGE II                  0                  1
  STAGE IIA                 2                 28
  STAGE IIB                 3                 13
  STAGE III                 0                 11
  STAGE IIIA                1                  7
  STAGE IIIB                2                  4
  STAGE IIIC                0                  3
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  12Q LOSS MUTATED       4  4     6
  12Q LOSS WILD-TYPE    15 22    44
D64V4, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1                4                 15
  T2                   4                 22
  T3+T4                6                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  12Q LOSS MUTATED    7  4     3
  12Q LOSS WILD-TYPE 43 29     8
D64V5, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0                   7                 43
  N1                   4                 29
  N2+N3                3                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  12Q LOSS MUTATED   11   0  3
  12Q LOSS WILD-TYPE 64   1 12
D64V6, multiclass
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                11                 64
  M1A                0                  1
  MX                 3                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    6  9
  12Q LOSS WILD-TYPE  9 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      6    9
  12Q LOSS WILD-TYPE    9   81
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                6                  9
  MALE                  9                 81
[1] 2 2
[1] FALSE
D64V8, continuous
D64V9, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    1 12
  12Q LOSS WILD-TYPE 34 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   12
  12Q LOSS WILD-TYPE   34   54
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                1                 34
  WHITE               12                 54
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   28  9
  13Q LOSS WILD-TYPE 39 22
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                37                 61 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 9                 22 
$`13Q LOSS MUTATED`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
       20.09         0.85        20.78         0.26         0.53        17.03 
TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-L5-A4OE TCGA-L5-A4OF 
        0.13        44.75        60.39        53.85         3.52         3.68 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A891 TCGA-L5-A8NU 
        6.41         4.08         3.16        29.00         3.95        83.24 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       10.36         0.07        10.45         0.07         0.33         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.13         0.07         0.07         0.13         0.07         0.10 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-R6-A6KZ TCGA-R6-A6XG 
        0.10         0.10         0.07         0.20         5.06        29.59 
TCGA-R6-A6XQ 
        6.35 

$`13Q LOSS WILD-TYPE`
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-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG 
        0.36         1.12         0.46       122.10         3.68        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       42.77         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-A8NJ TCGA-L5-A8NQ TCGA-LN-A49M TCGA-LN-A49V TCGA-LN-A49X 
        3.02        16.47        21.37         0.16         0.10         0.10 
TCGA-LN-A49Y TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-M9-A5M8 
        0.07         0.07         0.07         0.10         1.18        17.62 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         3.78         8.02         7.59        14.70         7.04 
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-A7RE 
        4.80 

  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 
              3.16               5.29 
[1] "0.1 - 83.2 (3.2)"  "0.0 - 122.1 (5.3)"
[1] "hr=" "1.3"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED         2        2        0        1        13         7
  13Q LOSS WILD-TYPE       5        2        4        0        17         9
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED           5          3          2          1        0
  13Q LOSS WILD-TYPE         6          5          4          2        1
D65V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   2                  5
  STAGE IA                  2                  2
  STAGE IB                  0                  4
  STAGE II                  1                  0
  STAGE IIA                13                 17
  STAGE IIB                 7                  9
  STAGE III                 5                  6
  STAGE IIIA                3                  5
  STAGE IIIB                2                  4
  STAGE IIIC                1                  2
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  13Q LOSS MUTATED       6 11    20
  13Q LOSS WILD-TYPE    13 15    30
D65V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1                6                 13
  T2                  11                 15
  T3+T4               20                 30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  13Q LOSS MUTATED   21 13     3
  13Q LOSS WILD-TYPE 29 20     8
D65V5, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                  21                 29
  N1                  13                 20
  N2+N3                3                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  13Q LOSS MUTATED   32   0  2
  13Q LOSS WILD-TYPE 43   1 13
D65V6, multiclass
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0                32                 43
  M1A                0                  1
  MX                 2                 13
[1] 3 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    3 37
  13Q LOSS WILD-TYPE 12 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3   37
  13Q LOSS WILD-TYPE   12   53
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                3                 12
  MALE                 37                 53
[1] 2 2
[1] FALSE
D65V8, continuous
D65V9, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   21 19
  13Q LOSS WILD-TYPE 14 47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     21   19
  13Q LOSS WILD-TYPE   14   47
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN               21                 14
  WHITE               19                 47
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   17  9
  14Q LOSS WILD-TYPE 50 22
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                26                 72 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 9                 22 
$`14Q LOSS MUTATED`
TCGA-IG-A3QL TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH 
       20.09         0.36         0.46       122.10        60.39        42.77 
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-A4OW TCGA-L5-A88S TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L7-A6VZ 
        7.13         6.94         0.36         3.95        16.47        10.36 
TCGA-LN-A49L TCGA-LN-A49W TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ 
       10.45         0.07        17.62         7.59         5.06         6.35 
TCGA-R6-A6Y2 TCGA-RE-A7BO 
        9.30         7.00 

$`14Q LOSS WILD-TYPE`
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-KH-A6WC 
        1.12        44.75        53.85         3.68        41.52         6.21 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16         3.45         4.31         8.78         6.41         4.08 
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-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        4.90        29.00         7.43         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M 
        7.40         3.02        21.37        83.24         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-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-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 
        1.18         5.16         3.78         8.02        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
       29.59        53.95         8.78        14.01         5.29         4.80 

  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 
             7.065              3.385 
[1] "0.1 - 122.1 (7.1)" "0.0 - 83.2 (3.4)" 
[1] "hr=" "1.2"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED         4        0        1        0         3         5
  14Q LOSS WILD-TYPE       3        4        3        1        27        11
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           3          0          3          1        0
  14Q LOSS WILD-TYPE         8          8          3          2        1
D66V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   4                  3
  STAGE IA                  0                  4
  STAGE IB                  1                  3
  STAGE II                  0                  1
  STAGE IIA                 3                 27
  STAGE IIB                 5                 11
  STAGE III                 3                  8
  STAGE IIIA                0                  8
  STAGE IIIB                3                  3
  STAGE IIIC                1                  2
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  14Q LOSS MUTATED       7  4    12
  14Q LOSS WILD-TYPE    12 22    38
D66V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1                7                 12
  T2                   4                 22
  T3+T4               12                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  14Q LOSS MUTATED   10  8     5
  14Q LOSS WILD-TYPE 40 25     6
D66V5, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                  10                 40
  N1                   8                 25
  N2+N3                5                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  14Q LOSS MUTATED   17   0  4
  14Q LOSS WILD-TYPE 58   1 11
D66V6, multiclass
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0                17                 58
  M1A                0                  1
  MX                 4                 11
[1] 3 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    5 22
  14Q LOSS WILD-TYPE 10 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      5   22
  14Q LOSS WILD-TYPE   10   68
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                5                 10
  MALE                 22                 68
[1] 2 2
[1] FALSE
D66V8, continuous
D66V9, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    5 19
  14Q LOSS WILD-TYPE 30 47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      5   19
  14Q LOSS WILD-TYPE   30   47
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                5                 30
  WHITE               19                 47
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   17  7
  15Q LOSS WILD-TYPE 50 24
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                24                 74 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 24 
$`15Q LOSS MUTATED`
TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A8O2 TCGA-L5-A43H 
       20.09        20.12         0.03         0.26         0.46         0.30 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OT 
        8.94         3.52         3.35        19.50         4.08         4.90 
TCGA-L5-A4OU TCGA-L5-A893 TCGA-L5-A8NU TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A5U6 
       29.00         3.02        83.24         0.10         0.10         0.20 
TCGA-LN-A5U7 TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RE 
        1.18         5.06        29.59         7.00         8.78         4.80 

$`15Q LOSS WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A50L 
       33.27         0.85        20.78         2.63         0.99         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 
       17.03         0.79         0.36         0.13         1.12       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        53.85         3.68        41.52        42.77 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OI 
        6.21         3.16         3.45         4.31         3.68         8.78 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
        6.41        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-A88V 
       30.74         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NQ 
       25.12         0.36         7.40         3.95        16.47        21.37 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         0.07        10.45         0.16         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-A4A6 TCGA-LN-A4A8 
        0.07         0.13         0.07         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A4MR 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-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59        14.70         7.04         6.35        53.95         9.30 
TCGA-S8-A6BW TCGA-V5-A7RB 
       14.01         5.29 

  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 
              4.44               4.13 
[1] "0.0 - 83.2 (4.4)"  "0.1 - 122.1 (4.1)"
[1] "hr=" "1.1"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED         3        1        1        0         5         4
  15Q LOSS WILD-TYPE       4        3        3        1        25        12
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED           3          2          3          0        1
  15Q LOSS WILD-TYPE         8          6          3          3        0
D67V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   3                  4
  STAGE IA                  1                  3
  STAGE IB                  1                  3
  STAGE II                  0                  1
  STAGE IIA                 5                 25
  STAGE IIB                 4                 12
  STAGE III                 3                  8
  STAGE IIIA                2                  6
  STAGE IIIB                3                  3
  STAGE IIIC                0                  3
  STAGE IV                  1                  0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  15Q LOSS MUTATED       6  5    13
  15Q LOSS WILD-TYPE    13 21    37
D67V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1                6                 13
  T2                   5                 21
  T3+T4               13                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  15Q LOSS MUTATED   11  9     4
  15Q LOSS WILD-TYPE 39 24     7
D67V5, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                  11                 39
  N1                   9                 24
  N2+N3                4                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  15Q LOSS MUTATED   19   1  2
  15Q LOSS WILD-TYPE 56   0 13
D67V6, multiclass
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0                19                 56
  M1A                1                  0
  MX                 2                 13
[1] 3 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    5 21
  15Q LOSS WILD-TYPE 10 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5   21
  15Q LOSS WILD-TYPE   10   69
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                5                 10
  MALE                 21                 69
[1] 2 2
[1] FALSE
D67V8, continuous
D67V9, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    7 18
  15Q LOSS WILD-TYPE 28 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7   18
  15Q LOSS WILD-TYPE   28   48
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                7                 28
  WHITE               18                 48
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED   19 10
  16P LOSS WILD-TYPE 48 21
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                29                 69 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                10                 21 
$`16P LOSS MUTATED`
TCGA-IG-A3YC TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH 
       20.12        42.77         3.16         3.52         3.35        19.50 
TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A88Y TCGA-L5-A88Z 
        6.41         3.16        30.74         4.90         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
        3.95         3.02        83.24        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-A7RE 
       53.95         9.30         7.00         5.29         4.80 

$`16P LOSS WILD-TYPE`
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-A625 
        0.26         0.99         0.53        17.03         0.79         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
        0.13         1.12         0.46       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       53.85         3.68        41.52         6.21         3.45         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON 
        4.31         8.94         3.68         8.78         4.08        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.32         7.17         1.38        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A8NJ TCGA-L5-A8NQ 
        6.94         8.71         2.60        25.12        16.47        21.37 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.36         0.07         0.16         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-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-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       17.62         3.78         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-S8-A6BV TCGA-S8-A6BW 
       29.59         8.78        14.01 

  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 
              5.16               3.68 
[1] "0.1 - 83.2 (5.2)"  "0.0 - 122.1 (3.7)"
[1] "hr=" "1"  
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P LOSS MUTATED         4        1        1        0         7         4
  16P LOSS WILD-TYPE       3        3        3        1        23        12
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED           1          1          2          0        1
  16P LOSS WILD-TYPE        10          7          4          3        0
D68V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   4                  3
  STAGE IA                  1                  3
  STAGE IB                  1                  3
  STAGE II                  0                  1
  STAGE IIA                 7                 23
  STAGE IIB                 4                 12
  STAGE III                 1                 10
  STAGE IIIA                1                  7
  STAGE IIIB                2                  4
  STAGE IIIC                0                  3
  STAGE IV                  1                  0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  16P LOSS MUTATED      10  7     8
  16P LOSS WILD-TYPE     9 19    42
D68V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1               10                  9
  T2                   7                 19
  T3+T4                8                 42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  16P LOSS MUTATED   13 10     2
  16P LOSS WILD-TYPE 37 23     9
D68V5, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                  13                 37
  N1                  10                 23
  N2+N3                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  16P LOSS MUTATED   20   1  3
  16P LOSS WILD-TYPE 55   0 12
D68V6, multiclass
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0                20                 55
  M1A                1                  0
  MX                 3                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    7 23
  16P LOSS WILD-TYPE  8 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7   23
  16P LOSS WILD-TYPE    8   67
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                7                  8
  MALE                 23                 67
[1] 2 2
[1] FALSE
D68V8, continuous
D68V9, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    7 22
  16P LOSS WILD-TYPE 28 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7   22
  16P LOSS WILD-TYPE   28   44
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                7                 28
  WHITE               22                 44
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   19 10
  16Q LOSS WILD-TYPE 48 21
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                29                 69 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                 21 
$`16Q LOSS MUTATED`
TCGA-IG-A3QL TCGA-IG-A3YC TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE 
       20.09        20.12        42.77         3.16         8.94         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-A891 TCGA-L5-A893 TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L 
        0.36         3.95         3.02        83.24        10.36        10.45 
TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A4MQ TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6XQ 
        0.33         0.10         0.10         5.16         5.06         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
       53.95         9.30         7.00         5.29         4.80 

$`16Q LOSS WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27         0.85        20.78         2.63         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-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        1.12         0.46       122.10        44.75        60.39        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
        3.68        41.52         6.21         3.45         0.30         4.31 
TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
        3.68         8.78         4.08        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        1.38        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-LN-A49K 
        2.60        25.12         7.40        16.47        21.37         0.07 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
        0.16         0.07         0.10         0.13         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-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10         0.07         0.07         0.07         0.20         1.18 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       17.62         3.78         8.02         7.59        14.70         7.04 
TCGA-R6-A6XG TCGA-S8-A6BV TCGA-S8-A6BW 
       29.59         8.78        14.01 

  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 
              5.29               3.45 
[1] "0.1 - 83.2 (5.3)"  "0.0 - 122.1 (3.5)"
[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        1        0         5         4
  16Q LOSS WILD-TYPE       3        3        3        1        25        12
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED           1          1          2          1        1
  16Q LOSS WILD-TYPE        10          7          4          2        0
D69V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   4                  3
  STAGE IA                  1                  3
  STAGE IB                  1                  3
  STAGE II                  0                  1
  STAGE IIA                 5                 25
  STAGE IIB                 4                 12
  STAGE III                 1                 10
  STAGE IIIA                1                  7
  STAGE IIIB                2                  4
  STAGE IIIC                1                  2
  STAGE IV                  1                  0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  16Q LOSS MUTATED       9  5    11
  16Q LOSS WILD-TYPE    10 21    39
D69V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1                9                 10
  T2                   5                 21
  T3+T4               11                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  16Q LOSS MUTATED   13  8     4
  16Q LOSS WILD-TYPE 37 25     7
D69V5, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                  13                 37
  N1                   8                 25
  N2+N3                4                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  16Q LOSS MUTATED   18   1  5
  16Q LOSS WILD-TYPE 57   0 10
D69V6, multiclass
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0                18                 57
  M1A                1                  0
  MX                 5                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    7 23
  16Q LOSS WILD-TYPE  8 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      7   23
  16Q LOSS WILD-TYPE    8   67
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                7                  8
  MALE                 23                 67
[1] 2 2
[1] FALSE
D69V8, continuous
D69V9, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    5 23
  16Q LOSS WILD-TYPE 30 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5   23
  16Q LOSS WILD-TYPE   30   43
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                5                 30
  WHITE               23                 43
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   22 14
  17P LOSS WILD-TYPE 45 17
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                36                 62 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                14                 17 
$`17P LOSS MUTATED`
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-L5-A43E 
        0.03         0.26         0.79       122.10        42.77         3.45 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OP 
        3.52         3.68         3.35        19.50         3.32         7.17 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 
        4.90         7.13         7.43         2.60         0.36         3.95 
TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49W 
       16.47        83.24         0.07        10.45         0.13         0.07 
TCGA-LN-A5U6 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 
        0.20        17.62         5.16         3.78         7.59         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RE 
       29.59         9.30         7.00         8.78        14.01         4.80 

$`17P LOSS WILD-TYPE`
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-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         1.12 
TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        0.46        44.75        60.39        53.85         3.68        41.52 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI 
        6.21         3.16         0.30         4.31         8.94         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-A4OU TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
       29.00         6.94         8.71        25.12         7.40         3.02 
TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       21.37        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-V5-A7RB 
       53.95         5.29 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.03               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            122.10              60.39 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              5.03               3.42 
[1] "0.0 - 122.1 (5.0)" "0.1 - 60.4 (3.4)" 
[1] "hr=" "1.2"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED         4        1        3        0         8         7
  17P LOSS WILD-TYPE       3        3        1        1        22         9
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED           3          1          4          1        1
  17P LOSS WILD-TYPE         8          7          2          2        0
D70V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   4                  3
  STAGE IA                  1                  3
  STAGE IB                  3                  1
  STAGE II                  0                  1
  STAGE IIA                 8                 22
  STAGE IIB                 7                  9
  STAGE III                 3                  8
  STAGE IIIA                1                  7
  STAGE IIIB                4                  2
  STAGE IIIC                1                  2
  STAGE IV                  1                  0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  17P LOSS MUTATED       9 10    16
  17P LOSS WILD-TYPE    10 16    34
D70V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1                9                 10
  T2                  10                 16
  T3+T4               16                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  17P LOSS MUTATED   17 13     5
  17P LOSS WILD-TYPE 33 20     6
D70V5, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                  17                 33
  N1                  13                 20
  N2+N3                5                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  17P LOSS MUTATED   27   1  5
  17P LOSS WILD-TYPE 48   0 10
D70V6, multiclass
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0                27                 48
  M1A                1                  0
  MX                 5                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    6 33
  17P LOSS WILD-TYPE  9 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      6   33
  17P LOSS WILD-TYPE    9   57
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                6                  9
  MALE                 33                 57
[1] 2 2
[1] FALSE
D70V8, continuous
D70V9, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    8 29
  17P LOSS WILD-TYPE 27 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      8   29
  17P LOSS WILD-TYPE   27   37
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                8                 27
  WHITE               29                 37
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    5  5
  17Q LOSS WILD-TYPE 62 26
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                10                 88 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                 26 
$`17Q LOSS MUTATED`
TCGA-IG-A5B8 TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A891 TCGA-LN-A49L TCGA-LN-A5U6 
        0.79         7.13         0.36         3.95        10.45         0.20 
TCGA-Q9-A6FU TCGA-R6-A6Y2 TCGA-S8-A6BW TCGA-V5-A7RE 
        5.16         9.30        14.01         4.80 

$`17Q LOSS WILD-TYPE`
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-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 
        0.03         0.26         0.99         0.53        17.03         0.36 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
        0.13         1.12         0.46       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A43C 
       53.85         3.68        41.52        42.77         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-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        30.74         4.90 
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-A893 TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ 
        7.40         3.02        16.47        21.37        83.24        10.36 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        0.07         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-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-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
       53.95         7.00         8.78         5.29 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.20               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             14.01             122.10 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              4.98               3.93 
[1] "0.2 - 14.0 (5.0)"  "0.0 - 122.1 (3.9)"
[1] "hr=" "2.1"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED         0        0        3        0         3         2
  17Q LOSS WILD-TYPE       7        4        1        1        27        14
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED           0          0          1          0        0
  17Q LOSS WILD-TYPE        11          8          5          3        1
D71V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   0                  7
  STAGE IA                  0                  4
  STAGE IB                  3                  1
  STAGE II                  0                  1
  STAGE IIA                 3                 27
  STAGE IIB                 2                 14
  STAGE III                 0                 11
  STAGE IIIA                0                  8
  STAGE IIIB                1                  5
  STAGE IIIC                0                  3
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  17Q LOSS MUTATED       2  5     4
  17Q LOSS WILD-TYPE    17 21    46
D71V4, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1                2                 17
  T2                   5                 21
  T3+T4                4                 46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  17Q LOSS MUTATED    7  3     1
  17Q LOSS WILD-TYPE 43 30    10
D71V5, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                   7                 43
  N1                   3                 30
  N2+N3                1                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  17Q LOSS MUTATED    9   0  2
  17Q LOSS WILD-TYPE 66   1 13
D71V6, multiclass
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                 9                 66
  M1A                0                  1
  MX                 2                 13
[1] 3 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    2 10
  17Q LOSS WILD-TYPE 13 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2   10
  17Q LOSS WILD-TYPE   13   80
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                2                 13
  MALE                 10                 80
[1] 2 2
[1] FALSE
D71V8, continuous
D71V9, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    4  7
  17Q LOSS WILD-TYPE 31 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    7
  17Q LOSS WILD-TYPE   31   59
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                4                 31
  WHITE                7                 59
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   21 13
  18P LOSS WILD-TYPE 46 18
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                34                 64 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                13                 18 
$`18P LOSS MUTATED`
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A5B8 TCGA-JY-A6FA TCGA-JY-A6FH 
       33.27         0.85         2.63         0.79        44.75        42.77 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.16         3.45         0.30         3.52         3.68         3.35 
TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 
       19.50         7.17         7.43         6.94         2.60         3.95 
TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       16.47        10.36         0.07        10.45         0.07         0.33 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.16         3.78         7.59        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        9.30         7.00         8.78         5.29 

$`18P LOSS WILD-TYPE`
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.09        20.78        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         1.12         0.46 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC 
      122.10        60.39        53.85         3.68        41.52         6.21 
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-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-A8NQ TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       21.37        83.24         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-A7RE 
       14.70         7.04        14.01         4.80 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.07               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             53.95             122.10 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              5.82               3.50 
[1] "0.1 - 54.0 (5.8)"  "0.0 - 122.1 (3.5)"
[1] "hr=" "1.2"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED         3        1        2        0         6         6
  18P LOSS WILD-TYPE       4        3        2        1        24        10
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED           4          3          3          1        0
  18P LOSS WILD-TYPE         7          5          3          2        1
D72V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   3                  4
  STAGE IA                  1                  3
  STAGE IB                  2                  2
  STAGE II                  0                  1
  STAGE IIA                 6                 24
  STAGE IIB                 6                 10
  STAGE III                 4                  7
  STAGE IIIA                3                  5
  STAGE IIIB                3                  3
  STAGE IIIC                1                  2
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  18P LOSS MUTATED       7  5    19
  18P LOSS WILD-TYPE    12 21    31
D72V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1                7                 12
  T2                   5                 21
  T3+T4               19                 31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  18P LOSS MUTATED   13 14     4
  18P LOSS WILD-TYPE 37 19     7
D72V5, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                  13                 37
  N1                  14                 19
  N2+N3                4                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  18P LOSS MUTATED   23   0  6
  18P LOSS WILD-TYPE 52   1  9
D72V6, multiclass
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0                23                 52
  M1A                0                  1
  MX                 6                  9
[1] 3 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    6 31
  18P LOSS WILD-TYPE  9 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      6   31
  18P LOSS WILD-TYPE    9   59
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                6                  9
  MALE                 31                 59
[1] 2 2
[1] FALSE
D72V8, continuous
D72V9, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    8 28
  18P LOSS WILD-TYPE 27 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      8   28
  18P LOSS WILD-TYPE   27   38
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                8                 27
  WHITE               28                 38
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   35 15
  18Q LOSS WILD-TYPE 32 16
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                50                 48 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                15                 16 
$`18Q LOSS MUTATED`
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A6QS 
        0.85         2.63         0.26         0.53         0.79         0.13 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M 
       44.75        53.85        42.77         3.16         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OP 
        3.52         3.68         3.35        19.50         3.32         7.17 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 
       29.00         7.43         6.94         2.60         3.95         3.02 
TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       16.47        83.24        10.36         0.07        10.45         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.07         0.33         0.10         0.07         0.10         0.10 
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-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-RE-A7BO 
        8.02         7.59        29.59         6.35        53.95         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB 
        8.78         5.29 

$`18Q LOSS WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
       33.27        20.09        20.78        20.12         0.03         0.99 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB 
       17.03         0.36         1.12         0.46       122.10        60.39 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OI 
        3.68        41.52         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-A4OT TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        4.90         7.13         8.71        25.12         0.36         7.40 
TCGA-L5-A8NQ TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
       21.37         0.13         0.07         0.10         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 
        0.13         0.07         0.10         0.07         0.07         1.18 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-S8-A6BW TCGA-V5-A7RE 
        5.06        14.70         7.04         9.30        14.01         4.80 

  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 
              3.73               4.85 
[1] "0.1 - 83.2 (3.7)"  "0.0 - 122.1 (4.8)"
[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        2        1        13         8
  18Q LOSS WILD-TYPE       4        3        2        0        17         8
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED           6          4          4          2        0
  18Q LOSS WILD-TYPE         5          4          2          1        1
D73V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   3                  4
  STAGE IA                  1                  3
  STAGE IB                  2                  2
  STAGE II                  1                  0
  STAGE IIA                13                 17
  STAGE IIB                 8                  8
  STAGE III                 6                  5
  STAGE IIIA                4                  4
  STAGE IIIB                4                  2
  STAGE IIIC                2                  1
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  18Q LOSS MUTATED       7 13    27
  18Q LOSS WILD-TYPE    12 13    23
D73V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1                7                 12
  T2                  13                 13
  T3+T4               27                 23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  18Q LOSS MUTATED   21 19     7
  18Q LOSS WILD-TYPE 29 14     4
D73V5, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                  21                 29
  N1                  19                 14
  N2+N3                7                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  18Q LOSS MUTATED   38   0  7
  18Q LOSS WILD-TYPE 37   1  8
D73V6, multiclass
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0                38                 37
  M1A                0                  1
  MX                 7                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    8 45
  18Q LOSS WILD-TYPE  7 45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      8   45
  18Q LOSS WILD-TYPE    7   45
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                8                  7
  MALE                 45                 45
[1] 2 2
[1] FALSE
D73V8, continuous
D73V9, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   18 32
  18Q LOSS WILD-TYPE 17 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     18   32
  18Q LOSS WILD-TYPE   17   34
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN               18                 17
  WHITE               32                 34
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED   23  8
  19P LOSS WILD-TYPE 44 23
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                31                 67 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 8                 23 
$`19P LOSS MUTATED`
TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A6QS TCGA-JY-A6F8 
        2.63         0.26         0.53        17.03         0.13       122.10 
TCGA-JY-A6FD TCGA-JY-A6FH TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OM 
       53.85        42.77         3.45         4.31         3.68         4.08 
TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49L 
        7.17        30.74         7.43        16.47        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 
        0.16         0.10         0.07         0.07         0.07         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 
        0.07         0.10         0.20         8.02         5.06         7.04 
TCGA-R6-A6XQ 
        6.35 

$`19P LOSS WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09         0.85        20.78        20.12         0.03 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6FA 
        0.99         0.79         0.36         1.12         0.46        44.75 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       60.39         3.68        41.52         6.21         3.16         0.30 
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-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-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.13         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49K 
        7.40         3.95         3.02        21.37        83.24         0.07 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A4 
        0.07         0.33         0.13         0.10         0.10         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-A6DQ TCGA-R6-A6L4 TCGA-R6-A6XG 
       17.62         5.16         3.78         7.59        14.70        29.59 
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-A7RE 
        4.80 

  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 
              4.08               4.80 
[1] "0.1 - 122.1 (4.1)" "0.0 - 83.2 (4.8)" 
[1] "hr=" "1.2"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED         2        2        0        1         9         8
  19P LOSS WILD-TYPE       5        2        4        0        21         8
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED           4          2          1          1        0
  19P LOSS WILD-TYPE         7          6          5          2        1
D74V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   2                  5
  STAGE IA                  2                  2
  STAGE IB                  0                  4
  STAGE II                  1                  0
  STAGE IIA                 9                 21
  STAGE IIB                 8                  8
  STAGE III                 4                  7
  STAGE IIIA                2                  6
  STAGE IIIB                1                  5
  STAGE IIIC                1                  2
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  19P LOSS MUTATED       6 10    14
  19P LOSS WILD-TYPE    13 16    36
D74V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1                6                 13
  T2                  10                 16
  T3+T4               14                 36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  19P LOSS MUTATED   15 13     2
  19P LOSS WILD-TYPE 35 20     9
D74V5, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                  15                 35
  N1                  13                 20
  N2+N3                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  19P LOSS MUTATED   25   0  3
  19P LOSS WILD-TYPE 50   1 12
D74V6, multiclass
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0                25                 50
  M1A                0                  1
  MX                 3                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    4 30
  19P LOSS WILD-TYPE 11 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4   30
  19P LOSS WILD-TYPE   11   60
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                4                 11
  MALE                 30                 60
[1] 2 2
[1] FALSE
D74V8, continuous
D74V9, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   15 19
  19P LOSS WILD-TYPE 20 47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     15   19
  19P LOSS WILD-TYPE   20   47
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN               15                 20
  WHITE               19                 47
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED   18  5
  19Q LOSS WILD-TYPE 49 26
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                23                 75 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 5                 26 
$`19Q LOSS MUTATED`
TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A6QS TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FH 
        2.63         0.53         0.13       122.10        53.85        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-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W 
        6.94        10.45         0.16         0.10         0.13         0.07 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A5U6 TCGA-R6-A6DN TCGA-R6-A6XQ 
        0.07         0.13         0.20         8.02         6.35 

$`19Q LOSS WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09         0.85        20.78        20.12         0.03 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP 
        0.26         0.99        17.03         0.79         0.36         1.12 
TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC 
        0.46        44.75        60.39         3.68        41.52         6.21 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.16         0.30         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-A4OQ 
       19.50         8.78         6.41        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88V 
        3.16         4.90        29.00         7.13         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ 
       25.12         0.36         7.40         3.95         3.02        16.47 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O 
       21.37        83.24        10.36         0.07         0.07         0.33 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.07         0.10         0.10         0.07         0.10         0.10 
TCGA-LN-A4A6 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-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       17.62         5.16         3.78         7.59         5.06        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-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
       14.01         5.29         4.80 

  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 
              4.08               4.80 
[1] "0.1 - 122.1 (4.1)" "0.0 - 83.2 (4.8)" 
[1] "hr=" "1.6"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED         2        2        1        0         9         6
  19Q LOSS WILD-TYPE       5        2        3        1        21        10
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED           2          2          0          0        0
  19Q LOSS WILD-TYPE         9          6          6          3        1
D75V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   2                  5
  STAGE IA                  2                  2
  STAGE IB                  1                  3
  STAGE II                  0                  1
  STAGE IIA                 9                 21
  STAGE IIB                 6                 10
  STAGE III                 2                  9
  STAGE IIIA                2                  6
  STAGE IIIB                0                  6
  STAGE IIIC                0                  3
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  19Q LOSS MUTATED       4  9    11
  19Q LOSS WILD-TYPE    15 17    39
D75V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1                4                 15
  T2                   9                 17
  T3+T4               11                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  19Q LOSS MUTATED   15  9     0
  19Q LOSS WILD-TYPE 35 24    11
D75V5, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                  15                 35
  N1                   9                 24
  N2+N3                0                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  19Q LOSS MUTATED   20   0  3
  19Q LOSS WILD-TYPE 55   1 12
D75V6, multiclass
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                20                 55
  M1A                0                  1
  MX                 3                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    4 22
  19Q LOSS WILD-TYPE 11 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      4   22
  19Q LOSS WILD-TYPE   11   68
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                4                 11
  MALE                 22                 68
[1] 2 2
[1] FALSE
D75V8, continuous
D75V9, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED   13 13
  19Q LOSS WILD-TYPE 22 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     13   13
  19Q LOSS WILD-TYPE   22   53
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN               13                 22
  WHITE               13                 53
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED   11  2
  20P LOSS WILD-TYPE 56 29
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                13                 85 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 29 
$`20P LOSS MUTATED`
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FH TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH 
       44.75        53.85        42.77         8.94         3.68        19.50 
TCGA-L5-A4OO TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49Y TCGA-R6-A6XG 
        3.32        83.24         0.16         0.33         0.07        29.59 
TCGA-S8-A6BW 
       14.01 

$`20P LOSS WILD-TYPE`
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-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-JY-A6F8 TCGA-JY-A6FB 
        0.36         0.13         1.12         0.46       122.10        60.39 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
        3.68        41.52         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-A8NJ 
       25.12         0.36         7.40         3.95         3.02        16.47 
TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49R 
       21.37        10.36         0.07        10.45         0.07         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 
        0.13         0.07         0.10         0.07         0.10         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-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 
        4.80 

  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               3.95 
[1] "0.1 - 83.2 (14.0)" "0.0 - 122.1 (4.0)"
[1] "hr=" "4.7"
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       6        4        3        1        24        13
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           1          0          0          1        0
  20P LOSS WILD-TYPE        10          8          6          2        1
D76V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   1                  6
  STAGE IA                  0                  4
  STAGE IB                  1                  3
  STAGE II                  0                  1
  STAGE IIA                 6                 24
  STAGE IIB                 3                 13
  STAGE III                 1                 10
  STAGE IIIA                0                  8
  STAGE IIIB                0                  6
  STAGE IIIC                1                  2
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  20P LOSS MUTATED       2  6     6
  20P LOSS WILD-TYPE    17 20    44
D76V4, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1                2                 17
  T2                   6                 20
  T3+T4                6                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  20P LOSS MUTATED    8  4     2
  20P LOSS WILD-TYPE 42 29     9
D76V5, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                   8                 42
  N1                   4                 29
  N2+N3                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  20P LOSS MUTATED   11   0  2
  20P LOSS WILD-TYPE 64   1 13
D76V6, multiclass
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                11                 64
  M1A                0                  1
  MX                 2                 13
[1] 3 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 13
  20P LOSS WILD-TYPE 13 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   13
  20P LOSS WILD-TYPE   13   77
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                2                 13
  MALE                 13                 77
[1] 2 2
[1] FALSE
D76V8, continuous
D76V9, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    7  7
  20P LOSS WILD-TYPE 28 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      7    7
  20P LOSS WILD-TYPE   28   59
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                7                 28
  WHITE                7                 59
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                 0  1
  20Q LOSS MUTATED    4  1
  20Q LOSS WILD-TYPE 63 30
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 5                 93 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 30 
$`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-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-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-JY-A6F8 TCGA-JY-A6FB 
        0.36         0.13         1.12         0.46       122.10        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       53.85         3.68        41.52         6.21         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         4.31         3.52         3.68         3.35        19.50 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
        8.78         6.41         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-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-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ 
        3.95         3.02        16.47        21.37        83.24        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-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-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-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        8.78         5.29         4.80 

  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               3.95 
[1] "3.3 - 44.8 (14.0)" "0.0 - 122.1 (4.0)"
[1] "hr=" "3.3"
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       7        4        3        1        29        14
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED           0          0          0          1        0
  20Q LOSS WILD-TYPE        11          8          6          2        1
D77V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                  7
  STAGE IA                  0                  4
  STAGE IB                  1                  3
  STAGE II                  0                  1
  STAGE IIA                 1                 29
  STAGE IIB                 2                 14
  STAGE III                 0                 11
  STAGE IIIA                0                  8
  STAGE IIIB                0                  6
  STAGE IIIC                1                  2
  STAGE IV                  0                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  20Q LOSS MUTATED       0  4     2
  20Q LOSS WILD-TYPE    19 22    48
D77V4, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1                0                 19
  T2                   4                 22
  T3+T4                2                 48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  20Q LOSS MUTATED    2  2     2
  20Q LOSS WILD-TYPE 48 31     9
D77V5, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                   2                 48
  N1                   2                 31
  N2+N3                2                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  20Q LOSS MUTATED    4   0  2
  20Q LOSS WILD-TYPE 71   1 13
D77V6, multiclass
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                 4                 71
  M1A                0                  1
  MX                 2                 13
[1] 3 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 14 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    5
  20Q LOSS WILD-TYPE   14   85
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                1                 14
  MALE                  5                 85
[1] 2 2
[1] FALSE
D77V8, continuous
D77V9, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    2  3
  20Q LOSS WILD-TYPE 33 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    3
  20Q LOSS WILD-TYPE   33   63
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                2                 33
  WHITE                3                 63
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   39 18
  21Q LOSS WILD-TYPE 28 13
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                57                 41 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                18                 13 
$`21Q LOSS MUTATED`
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-L5-A43C TCGA-L5-A43E 
        0.53         0.79         0.13       122.10         3.16         3.45 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         4.31         8.94         3.52         3.35        19.50 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        6.41         4.08         7.17         3.16        30.74         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y 
       29.00         7.13         7.43         6.94         2.60         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49K 
        7.40         3.95         3.02        16.47        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 
        6.35         9.30         4.80 

$`21Q LOSS WILD-TYPE`
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP 
       20.09         2.63         0.99        17.03         0.36         1.12 
TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        0.46        44.75        60.39        53.85         3.68        41.52 
TCGA-JY-A6FH TCGA-KH-A6WC TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO 
       42.77         6.21         3.68         8.78        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L 
        1.38         8.71        25.12        21.37        83.24        10.45 
TCGA-LN-A49M TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        0.16         0.07         0.10         0.10         0.07         0.13 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 TCGA-R6-A6L4 
        0.10         0.10         0.07         0.07         1.18        14.70 
TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
       53.95         7.00         8.78        14.01         5.29 

  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 
              4.08               5.29 
[1] "0.0 - 122.1 (4.1)" "0.1 - 83.2 (5.3)" 
[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        3        1        11         8
  21Q LOSS WILD-TYPE       1        1        1        0        19         8
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED           8          4          4          1        1
  21Q LOSS WILD-TYPE         3          4          2          2        0
D78V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   6                  1
  STAGE IA                  3                  1
  STAGE IB                  3                  1
  STAGE II                  1                  0
  STAGE IIA                11                 19
  STAGE IIB                 8                  8
  STAGE III                 8                  3
  STAGE IIIA                4                  4
  STAGE IIIB                4                  2
  STAGE IIIC                1                  2
  STAGE IV                  1                  0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  21Q LOSS MUTATED      12 12    29
  21Q LOSS WILD-TYPE     7 14    21
D78V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1               12                  7
  T2                  12                 14
  T3+T4               29                 21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  21Q LOSS MUTATED   27 20     6
  21Q LOSS WILD-TYPE 23 13     5
D78V5, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                  27                 23
  N1                  20                 13
  N2+N3                6                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  21Q LOSS MUTATED   42   1  8
  21Q LOSS WILD-TYPE 33   0  7
D78V6, multiclass
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0                42                 33
  M1A                1                  0
  MX                 8                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   12 49
  21Q LOSS WILD-TYPE  3 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     12   49
  21Q LOSS WILD-TYPE    3   41
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               12                  3
  MALE                 49                 41
[1] 2 2
[1] FALSE
D78V8, continuous
D78V9, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   16 42
  21Q LOSS WILD-TYPE 19 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     16   42
  21Q LOSS WILD-TYPE   19   24
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN               16                 19
  WHITE               42                 24
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   24 12
  22Q LOSS WILD-TYPE 43 19
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                36                 62 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                12                 19 
$`22Q LOSS MUTATED`
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A8O2 
        2.63         0.03         0.26         0.53         0.79         0.46 
TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH 
      122.10        42.77         3.16         3.52         3.35        19.50 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A88Z 
       30.74         4.90        29.00         7.13         0.36         7.40 
TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O 
        3.02        16.47        10.36         0.07        10.45         0.33 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-R6-A6DN 
        0.10         0.07         0.07         0.10         0.07         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
        7.59         5.06        29.59         7.00         5.29         4.80 

$`22Q LOSS WILD-TYPE`
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT 
       33.27        20.09         0.85        20.78        20.12         0.99 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FB 
       17.03         0.36         0.13         1.12        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       53.85         3.68        41.52         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-A8NQ 
        6.94         8.71         2.60        25.12         3.95        21.37 
TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49Y 
       83.24         0.16         0.07         0.13         0.10         0.07 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.13         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-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-S8-A6BV TCGA-S8-A6BW 
        8.78        14.01 

  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 
             4.160              4.195 
[1] "0.0 - 122.1 (4.2)" "0.1 - 83.2 (4.2)" 
[1] "hr=" "1.2"
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED         4        0        2        0         9         5
  22Q LOSS WILD-TYPE       3        4        2        1        21        11
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED           5          2          3          1        1
  22Q LOSS WILD-TYPE         6          6          3          2        0
D79V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   4                  3
  STAGE IA                  0                  4
  STAGE IB                  2                  2
  STAGE II                  0                  1
  STAGE IIA                 9                 21
  STAGE IIB                 5                 11
  STAGE III                 5                  6
  STAGE IIIA                2                  6
  STAGE IIIB                3                  3
  STAGE IIIC                1                  2
  STAGE IV                  1                  0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3+T4
  22Q LOSS MUTATED       9  7    18
  22Q LOSS WILD-TYPE    10 19    32
D79V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1                9                 10
  T2                   7                 19
  T3+T4               18                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2+N3
  22Q LOSS MUTATED   15 15     4
  22Q LOSS WILD-TYPE 35 18     7
D79V5, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                  15                 35
  N1                  15                 18
  N2+N3                4                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1A MX
  22Q LOSS MUTATED   29   1  3
  22Q LOSS WILD-TYPE 46   0 12
D79V6, multiclass
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0                29                 46
  M1A                1                  0
  MX                 3                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    7 32
  22Q LOSS WILD-TYPE  8 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      7   32
  22Q LOSS WILD-TYPE    8   58
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                7                  8
  MALE                 32                 58
[1] 2 2
[1] FALSE
D79V8, continuous
D79V9, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   13 24
  22Q LOSS WILD-TYPE 22 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     13   24
  22Q LOSS WILD-TYPE   22   42
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN               13                 22
  WHITE               24                 42
[1] 2 2
[1] FALSE

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   16  6
  XQ LOSS WILD-TYPE 51 25
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               22                76 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                6                25 
$`XQ LOSS MUTATED`
TCGA-IG-A625 TCGA-JY-A6FA TCGA-JY-A6FH TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OJ 
        0.36        44.75        42.77         3.45         3.52         6.41 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A891 TCGA-L5-A8NJ TCGA-LN-A49M 
       18.35         7.17         3.16         3.95        16.47         0.16 
TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 
        0.10         0.07         0.10         0.07         0.07         1.18 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-V5-A7RE 
       17.62         8.02         5.06         4.80 

$`XQ LOSS WILD-TYPE`
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-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-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD 
        0.13         1.12         0.46       122.10        60.39        53.85 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J 
        3.68        41.52         6.21         3.16         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM 
        8.94         3.68         3.35        19.50         8.78         4.08 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        3.32         1.38        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-A8NQ TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K 
        7.40         3.02        21.37        83.24        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-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
        0.07         0.10         0.13         0.07         0.10         0.10 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ 
        0.07         0.10         0.20         5.16         3.78         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-S8-A6BW TCGA-V5-A7RB 
        7.00         8.78        14.01         5.29 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.07              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            44.75            122.10 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            3.735             4.605 
[1] "0.1 - 44.8 (3.7)"  "0.0 - 122.1 (4.6)"
[1] "hr=" "1"  
D80V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ LOSS MUTATED         2        2        1        0         9         3
  XQ LOSS WILD-TYPE       5        2        3        1        21        13
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED           2          0          2          0        0
  XQ LOSS WILD-TYPE         9          8          4          3        1
D80V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  2                 5
  STAGE IA                 2                 2
  STAGE IB                 1                 3
  STAGE II                 0                 1
  STAGE IIA                9                21
  STAGE IIB                3                13
  STAGE III                2                 9
  STAGE IIIA               0                 8
  STAGE IIIB               2                 4
  STAGE IIIC               0                 3
  STAGE IV                 0                 1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3+T4
  XQ LOSS MUTATED       6  9     7
  XQ LOSS WILD-TYPE    13 17    43
D80V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1               6                13
  T2                  9                17
  T3+T4               7                43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2+N3
  XQ LOSS MUTATED   14  6     2
  XQ LOSS WILD-TYPE 36 27     9
D80V5, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0                 14                36
  N1                  6                27
  N2+N3               2                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1A MX
  XQ LOSS MUTATED   18   0  2
  XQ LOSS WILD-TYPE 57   1 13
D80V6, multiclass
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0               18                57
  M1A               0                 1
  MX                2                13
[1] 3 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    2 22
  XQ LOSS WILD-TYPE 13 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   22
  XQ LOSS WILD-TYPE   13   68
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               2                13
  MALE                22                68
[1] 2 2
[1] FALSE
D80V8, continuous
D80V9, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   11 12
  XQ LOSS WILD-TYPE 24 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     11   12
  XQ LOSS WILD-TYPE   24   54
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN              11                24
  WHITE              12                54
[1] 2 2
[1] FALSE
