[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"        "-oTSARC-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/SARC-TP/10006228/SARC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SARC-TP/10013801/transformed.cor.cli.txt"

nPatients in clinical file=114, in cluster file=169, common to both=114
[1]  80 114
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               21                93 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               21                93 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               23                91 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               23                91 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10               104 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10               104 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7               107 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7               107 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               12               102 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               12               102 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               11               103 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               11               103 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               23                91 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               23                91 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               17                97 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               17                97 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               36                78 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               36                78 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               30                84 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               30                84 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               22                92 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               22                92 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               21                93 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               21                93 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               29                85 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               29                85 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               25                89 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               25                89 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               25                89 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               25                89 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               29                85 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               29                85 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               19                95 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               19                95 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               26                88 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               26                88 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                10                104 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                10                104 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                110 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                110 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                108 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                108 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                109 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                109 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                13                101 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                13                101 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 8                106 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 8                106 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                108 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                108 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                21                 93 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                21                 93 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                29                 85 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                29                 85 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                17                 97 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                17                 97 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                108 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                108 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                22                 92 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                22                 92 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                16                 98 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                16                 98 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                17                 97 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                17                 97 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                16                 98 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                16                 98 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                33                 81 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                33                 81 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                22                 92 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                22                 92 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                28                 86 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                28                 86 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                35                 79 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                35                 79 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                26                 88 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                26                 88 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                26                 88 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                26                 88 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               14               100 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               14               100 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               16                98 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               16                98 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               16                98 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               16                98 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               32                82 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               32                82 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               27                87 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               27                87 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               20                94 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               20                94 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               24                90 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               24                90 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               18                96 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               18                96 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               22                92 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               22                92 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9               105 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9               105 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               15                99 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               15                99 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               28                86 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               28                86 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               17                97 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               17                97 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               16                98 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               16                98 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               14               100 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               14               100 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               24                90 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               24                90 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               14               100 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               14               100 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               34                80 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               34                80 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               23                91 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               23                91 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                52                 62 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                52                 62 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                62                 52 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                62                 52 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                44                 70 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                44                 70 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                36                 78 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                36                 78 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                25                 89 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                25                 89 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                26                 88 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                26                 88 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                55                 59 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                55                 59 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                30                 84 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                30                 84 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                17                 97 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                17                 97 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                33                 81 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                33                 81 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                59                 55 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                59                 55 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                22                 92 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                22                 92 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                22                 92 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                22                 92 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                27                 87 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                27                 87 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                28                 86 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                28                 86 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 7                107 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 7                107 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                17                 97 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                17                 97 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                 96 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                 96 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                106 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                106 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                19                 95 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                19                 95 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                33                 81 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                33                 81 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               42                72 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               42                72 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DCCUPLOADDATE"                         
 [6] "GENDER"                                
 [7] "RADIATIONTHERAPY"                      
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[11] "BATCHNUMBER"                           

Input Data has 11 rows and 114 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
          NA           62          827           NA          745           NA 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
        1420         1291          960          908         2271           NA 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
          NA           NA           NA           NA         1834          261 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
          NA         1620         1309           NA          702         2144 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
        3289          520          610          458          540         1301 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
          NA           NA           NA         1352         1197          876 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
          NA         1952           NA          587           NA          373 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
         828          455          805         2212          763          349 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
        1669          328          496           63          224           51 
TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
          NA           14            3            2            2          818 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
          NA          126           NA          729            3         1257 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
         298           NA          650          272           98           42 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
         217           NA           NA          966           NA         4362 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
        3555           NA         2229           NA          688          191 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I 
          NA           NA         2181         1107          356          160 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
          72           15          173          136          337            3 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
         124         2297           NA           NA           NA           NA 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
          NA           56           NA           NA          553          639 
TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
          NA          402           22           NA          826          259 
Variable 1:'AGE':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=75,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'BATCH.NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER" "RACE"  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 114 columns, 1 survival variables, and 3 non-survival variables.
AGE, nv=48, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED   12  9
  1P GAIN WILD-TYPE 66 27
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               21                93 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                9                27 
$`1P GAIN MUTATED`
TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3U9 TCGA-DX-A48K TCGA-DX-A48L TCGA-FX-A2QS 
        9.70        23.08        14.99        19.30        24.26         0.46 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       26.89         4.57         4.14        41.33         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-JV-A5VF TCGA-KF-A41W 
        8.94         7.13        25.22        31.76         1.05        11.70 
TCGA-N1-A6IA TCGA-PC-A5DM TCGA-SG-A6Z7 
        4.08         6.35         3.88 

$`1P GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        42.44        31.56        29.85        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       53.26        43.04         9.04        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
       20.05        15.06        17.75        42.77         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        54.87        10.78        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A5W3 
        1.68        16.18         0.10         0.07         0.07        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ 
       23.97         0.10        21.37         3.22         1.38        37.12 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I 
       22.62         6.28         3.91        71.70        36.39         5.26 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
        2.37         0.49         5.69         4.47        11.08         0.10 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 
       75.52        37.55        38.63        81.01        18.08         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU 
       46.82        18.08        18.18        21.01        13.22         0.72 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       18.08        27.16         8.52 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.46              0.07 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            80.48            143.41 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             9.80             18.08 
[1] "0.5 - 80.5 (9.8)"   "0.1 - 143.4 (18.1)"
[1] "hr=" "2.2"
D1V2, continuous
D1V3, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   13  8
  1P GAIN WILD-TYPE 49 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     13    8
  1P GAIN WILD-TYPE   49   44
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              13                49
  MALE                 8                44
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       0                         3    15
  1P GAIN WILD-TYPE     4                         5    62
D1V4, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               3                 5
  WHITE                                  15                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   17  6
  1Q GAIN WILD-TYPE 61 30
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               23                91 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                6                30 
$`1Q GAIN MUTATED`
TCGA-DX-A1L2 TCGA-DX-A3LT TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K 
       42.44        23.08        14.99        28.80        64.18        19.30 
TCGA-DX-A48O TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
       27.22        26.89         4.14         0.10        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IW-A3M6 
       80.48         8.94         7.13        25.22        31.76        22.62 
TCGA-KF-A41W TCGA-PC-A5DN TCGA-SG-A6Z7 TCGA-X6-A7WB TCGA-X6-A7WC 
       11.70        38.63         3.88        18.08        27.16 

$`1Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       46.68        31.56        29.85        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       53.26        43.04         9.04        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
       20.05        15.06        17.75        42.77         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N 
       44.45        39.35        34.88         9.73        24.26        12.26 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        26.47        72.72        25.08        11.47        54.87 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       10.78        16.31         2.07         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A5W3 
        0.46         0.10         0.07         0.07         4.57        12.62 
TCGA-HS-A5N7 TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K6 
       23.97        21.37         3.22         1.38        37.12        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE 
      143.41       116.88        13.58        73.28         5.92         6.28 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 
        1.05         3.91        71.70        36.39         5.26         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA 
        0.49         5.69         4.47        11.08         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 
       75.52        37.55         6.35        81.01        18.08         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU 
       46.82        18.08        18.18        21.01        13.22         0.72 
TCGA-X6-A7WD 
        8.52 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.10              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            80.48            143.41 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            23.08             16.18 
[1] "0.1 - 80.5 (23.1)"  "0.1 - 143.4 (16.2)"
[1] "hr=" "1.3"
D2V2, continuous
D2V3, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   15  8
  1Q GAIN WILD-TYPE 47 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     15    8
  1Q GAIN WILD-TYPE   47   44
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              15                47
  MALE                 8                44
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       1                         1    17
  1Q GAIN WILD-TYPE     3                         7    60
D2V4, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               1                 7
  WHITE                                  17                60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    6  4
  2P GAIN WILD-TYPE 72 32
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10               104 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                4                32 
$`2P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A23R TCGA-DX-A3LT TCGA-FX-A2QS TCGA-IW-A3M5 
       14.04         2.04        74.66        23.08         0.46         5.92 
TCGA-KF-A41W TCGA-MO-A47R TCGA-PC-A5DL TCGA-SG-A6Z7 
       11.70         0.10        37.55         3.88 

$`2P GAIN WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       27.19        12.85        24.49        18.54        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       31.56        29.85         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        53.26        43.04 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
        9.04        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       25.08        11.47        54.87        10.78        16.31         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
        7.36         1.68        16.18         0.10         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       26.89         4.57         4.14        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
       41.33         9.80        80.48        21.37         8.94         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        1.38         7.13        37.12        25.22        31.76        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE 
      143.41       116.88        13.58        73.28        22.62         6.28 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 
        1.05         3.91        71.70        36.39         5.26         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-N1-A6IA TCGA-PC-A5DK 
        0.49         5.69         4.47        11.08         4.08        75.52 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 
        6.35        38.63        81.01        18.08         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB 
       18.08        18.18        21.01        13.22         0.72        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD 
       27.16         8.52 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.10              0.07 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            74.66            143.41 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             8.81             18.08 
[1] "0.1 - 74.7 (8.8)"   "0.1 - 143.4 (18.1)"
[1] "hr=" "2.2"
D3V2, continuous
D3V3, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    6  4
  2P GAIN WILD-TYPE 56 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      6    4
  2P GAIN WILD-TYPE   56   48
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               6                56
  MALE                 4                48
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       1                         0     7
  2P GAIN WILD-TYPE     3                         8    70
D3V4, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               0                 8
  WHITE                                   7                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    6  1
  2Q GAIN WILD-TYPE 72 35
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7               107 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                1                35 
$`2Q GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A6BA TCGA-KF-A41W 
       14.04         2.04        74.66        23.08        54.87        11.70 
TCGA-MO-A47R 
        0.10 

$`2Q GAIN WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       27.19        12.85        24.49        18.54        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       31.56        29.85         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        53.26        43.04 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
        9.04        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       25.08        11.47        10.78        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
        1.68        16.18         0.46         0.10         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       26.89         4.57         4.14        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
       41.33         9.80        80.48        21.37         8.94         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        1.38         7.13        37.12        25.22        31.76        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
      143.41       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I 
        6.28         1.05         3.91        71.70        36.39         5.26 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-N1-A6IA 
        2.37         0.49         5.69         4.47        11.08         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
       75.52        37.55         6.35        38.63        81.01        18.08 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 
        1.84        46.82        18.08        18.18        21.01         3.88 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       13.22         0.72        18.08        27.16         8.52 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.10              0.07 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            74.66            143.41 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            14.04             18.08 
[1] "0.1 - 74.7 (14.0)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "2.1"
D4V2, continuous
D4V3, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    4  3
  2Q GAIN WILD-TYPE 58 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4    3
  2Q GAIN WILD-TYPE   58   49
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               4                58
  MALE                 3                49
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       1                         0     4
  2Q GAIN WILD-TYPE     3                         8    73
D4V4, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               0                 8
  WHITE                                   4                73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    8  4
  3P GAIN WILD-TYPE 70 32
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               12               102 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                32 
$`3P GAIN MUTATED`
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UF TCGA-HB-A2OT TCGA-IE-A3OV TCGA-IE-A4EI 
       42.77         4.54        64.18        26.89        80.48         8.94 
TCGA-IF-A4AJ TCGA-KF-A41W TCGA-MJ-A68H TCGA-PC-A5DP TCGA-UE-A6QU TCGA-X6-A7WC 
       25.22        11.70         4.47        18.08         0.72        27.16 

$`3P GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        42.44        31.56        29.85        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        53.26        43.04         9.04        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U9 
      108.13        17.10        20.05        15.06        17.75        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       10.68        44.45        39.35        28.80        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       19.30        24.26        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       72.72        25.08        11.47        54.87        10.78        16.31 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ 
        2.07         7.36         1.68        16.18         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07         0.07         4.57         4.14        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK 
        0.10        41.33         9.80        21.37         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        7.13        37.12        31.76        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
       13.58        73.28         5.92        22.62         6.28         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA 
        3.91        71.70        36.39         5.26         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
        5.69        11.08         0.10         4.08        75.52        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
        6.35        38.63        81.01         1.84        46.82        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WD 
       18.18        21.01         3.88        13.22        18.08         8.52 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.72              0.07 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            80.48            143.41 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           21.650            17.425 
[1] "0.7 - 80.5 (21.6)"  "0.1 - 143.4 (17.4)"
[1] "hr=" "1"  
D5V2, continuous
D5V3, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    7  5
  3P GAIN WILD-TYPE 55 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      7    5
  3P GAIN WILD-TYPE   55   47
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               7                55
  MALE                 5                47
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       1                         2     8
  3P GAIN WILD-TYPE     3                         6    69
D5V4, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               2                 6
  WHITE                                   8                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    8  3
  3Q GAIN WILD-TYPE 70 33
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               11               103 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                33 
$`3Q GAIN MUTATED`
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UF TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-IE-A4EI 
       42.77         4.54        64.18        26.89         0.10         8.94 
TCGA-IF-A4AJ TCGA-KF-A41W TCGA-PC-A5DP TCGA-UE-A6QU TCGA-X6-A7WC 
       25.22        11.70        18.08         0.72        27.16 

$`3Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        42.44        31.56        29.85        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        53.26        43.04         9.04        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U9 
      108.13        17.10        20.05        15.06        17.75        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       10.68        44.45        39.35        28.80        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       19.30        24.26        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       72.72        25.08        11.47        54.87        10.78        16.31 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ 
        2.07         7.36         1.68        16.18         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07         0.07         4.57         4.14        12.62        23.97 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK 
       41.33         9.80        80.48        21.37         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        7.13        37.12        31.76        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
       13.58        73.28         5.92        22.62         6.28         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA 
        3.91        71.70        36.39         5.26         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
        5.69         4.47        11.08         0.10         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       37.55         6.35        38.63        81.01         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WB 
       18.08        18.18        21.01         3.88        13.22        18.08 
TCGA-X6-A7WD 
        8.52 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.10              0.07 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            64.18            143.41 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            18.08             17.75 
[1] "0.1 - 64.2 (18.1)"  "0.1 - 143.4 (17.8)"
[1] "hr=" "1.1"
D6V2, continuous
D6V3, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    7  4
  3Q GAIN WILD-TYPE 55 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      7    4
  3Q GAIN WILD-TYPE   55   48
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               7                55
  MALE                 4                48
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       1                         1     7
  3Q GAIN WILD-TYPE     3                         7    70
D6V4, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               1                 7
  WHITE                                   7                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED   16  7
  4P GAIN WILD-TYPE 62 29
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               23                91 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                7                29 
$`4P GAIN MUTATED`
TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A48K TCGA-DX-A6BA 
       27.19        18.54        46.68        74.66        19.30        54.87 
TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-JV-A5VE 
        4.57        41.33         7.13        25.22       143.41         6.28 
TCGA-KF-A41W TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QQ-A5VA 
       11.70         4.47         4.08        37.55        81.01        18.08 
TCGA-QQ-A5VC TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WC 
       18.18         3.88        13.22         0.72        27.16 

$`4P GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04         2.04        12.85        24.49        42.44        31.56 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       29.85         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        53.26        43.04         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L 
       39.35        28.80        34.88        64.18         9.73        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       11.47        10.78        16.31         2.07         7.36         1.68 
TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
       16.18         0.46         0.10         0.07         0.07        26.89 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
        4.14        12.62        23.97         0.10         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AK 
       21.37         8.94         3.22         1.38        37.12        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
       28.21       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 
        1.05         3.91        71.70        36.39         5.26         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DM 
        0.49         5.69        11.08         0.10        75.52         6.35 
TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD TCGA-X6-A7WB 
       38.63        18.08         1.84        46.82        21.01        18.08 
TCGA-X6-A7WD 
        8.52 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.72              0.07 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           143.41            116.88 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            18.54             16.31 
[1] "0.7 - 143.4 (18.5)" "0.1 - 116.9 (16.3)"
[1] "hr=" "1.3"
D7V2, continuous
D7V3, binary
                   cls
clus                 0  1
  4P GAIN MUTATED   16  7
  4P GAIN WILD-TYPE 46 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     16    7
  4P GAIN WILD-TYPE   46   45
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              16                46
  MALE                 7                45
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       2                         3    13
  4P GAIN WILD-TYPE     2                         5    64
D7V4, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   2                 2
  BLACK OR AFRICAN AMERICAN               3                 5
  WHITE                                  13                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED   11  6
  4Q GAIN WILD-TYPE 67 30
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               17                97 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6                30 
$`4Q GAIN MUTATED`
TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A3LY TCGA-DX-A48K TCGA-HB-A3YV 
       27.19        18.54        46.68        17.10        19.30         4.57 
TCGA-HS-A5N9 TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-JV-A5VE 
       41.33         3.22         7.13        25.22       143.41         6.28 
TCGA-MJ-A68H TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QQ-A5VA TCGA-UE-A6QT 
        4.47        37.55        81.01        18.08        13.22 

$`4Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04         2.04        12.85        24.49        42.44        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       29.85        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        53.26        43.04 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 
        9.04        23.08        70.49       108.13        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L 
       39.35        28.80        34.88        64.18         9.73        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        54.87        10.78        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
        1.68        16.18         0.46         0.10         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
       26.89         4.14        12.62        23.97         0.10         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AK 
       80.48        21.37         8.94         1.38        37.12        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
       28.21       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I 
        1.05         3.91        71.70        36.39        11.70         5.26 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA 
        2.37         0.49         5.69        11.08         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       75.52         6.35        38.63        18.08         1.84        46.82 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC 
       18.18        21.01         3.88         0.72        18.08        27.16 
TCGA-X6-A7WD 
        8.52 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             3.22              0.07 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           143.41            116.88 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            18.54             16.31 
[1] "3.2 - 143.4 (18.5)" "0.1 - 116.9 (16.3)"
[1] "hr=" "1.1"
D8V2, continuous
D8V3, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED   10  7
  4Q GAIN WILD-TYPE 52 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     10    7
  4Q GAIN WILD-TYPE   52   45
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              10                52
  MALE                 7                45
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       1                         2    10
  4Q GAIN WILD-TYPE     3                         6    67
D8V4, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               2                 6
  WHITE                                  10                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   25 11
  5P GAIN WILD-TYPE 53 25
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               36                78 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11                25 
$`5P GAIN MUTATED`
TCGA-DX-A1KX TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A23Y TCGA-DX-A3LY TCGA-DX-A3U7 
       27.19        46.68        31.56         6.28        17.10        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48P 
        4.54        14.99        28.80        64.18        24.26        14.96 
TCGA-DX-A48R TCGA-DX-A6BG TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A4EI 
       26.47         7.36        26.89         4.57         0.10         8.94 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-K1-A3PN TCGA-LI-A67I 
        3.22         7.13        25.22        31.76        71.70         5.26 
TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A5V9 
        4.47         0.10         4.08         6.35        18.08        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WC 
       18.08        18.18         3.88        13.22         0.72        27.16 

$`5P GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 
       14.04         2.04        12.85        24.49        18.54        42.44 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       29.85        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        53.26        43.04         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       23.08        70.49       108.13        20.05        15.06        17.75 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       10.68        44.45        39.35        34.88         9.73        19.30 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       12.26        27.22        72.72        25.08        11.47        54.87 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS 
       10.78        16.31         2.07         1.68        16.18         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.10         0.07         0.07         4.14        12.62        23.97 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ 
       41.33         9.80        80.48        21.37         1.38        37.12 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-KF-A41W 
       22.62         6.28         1.05         3.91        36.39        11.70 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-PC-A5DK TCGA-PC-A5DL 
        2.37         0.49         5.69        11.08        75.52        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5VD TCGA-X6-A7WB TCGA-X6-A7WD 
       38.63        81.01         1.84        21.01        18.08         8.52 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.10              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            71.70            143.41 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           16.045            18.310 
[1] "0.1 - 71.7 (16.0)"  "0.1 - 143.4 (18.3)"
[1] "hr=" "1.4"
D9V2, continuous
D9V3, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   22 14
  5P GAIN WILD-TYPE 40 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     22   14
  5P GAIN WILD-TYPE   40   38
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              22                40
  MALE                14                38
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       3                         3    24
  5P GAIN WILD-TYPE     1                         5    53
D9V4, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   3                 1
  BLACK OR AFRICAN AMERICAN               3                 5
  WHITE                                  24                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED   19 11
  5Q GAIN WILD-TYPE 59 25
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               30                84 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               11                25 
$`5Q GAIN MUTATED`
TCGA-DX-A1KX TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A23Y TCGA-DX-A3U8 TCGA-DX-A3U9 
       27.19        46.68        31.56         6.28         4.54        14.99 
TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A6BK 
       28.80        64.18        24.26        14.96        26.47        16.18 
TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AK 
        4.57         0.10        80.48         8.94         3.22        31.76 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-LI-A67I TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA 
      143.41        13.58         5.26         4.47         0.10         4.08 
TCGA-PC-A5DM TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU 
        6.35        18.08        18.18         3.88        13.22         0.72 

$`5Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 
       14.04         2.04        12.85        24.49        18.54        42.44 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       29.85        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        53.26        43.04         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE 
       17.75        42.77        10.68        44.45        39.35        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V 
        9.73        19.30        12.26        27.22        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        54.87        10.78        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
        1.68         0.46         0.10         0.07         0.07        26.89 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH 
        4.14        12.62        23.97        41.33         9.80        21.37 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K8 
        1.38         7.13        37.12        25.22        28.21       116.88 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       73.28         5.92        22.62         6.28         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       71.70        36.39        11.70         2.37         0.49         5.69 
TCGA-MJ-A68J TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
       11.08        75.52        37.55        38.63        81.01        18.08 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        1.84        46.82        21.01        18.08        27.16         8.52 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.10              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           143.41            116.88 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            14.27             18.92 
[1] "0.1 - 143.4 (14.3)" "0.1 - 116.9 (18.9)"
[1] "hr=" "1.6"
D10V2, continuous
D10V3, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   21  9
  5Q GAIN WILD-TYPE 41 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     21    9
  5Q GAIN WILD-TYPE   41   43
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              21                41
  MALE                 9                43
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       3                         2    19
  5Q GAIN WILD-TYPE     1                         6    58
D10V4, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   3                 1
  BLACK OR AFRICAN AMERICAN               2                 6
  WHITE                                  19                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   14  8
  6P GAIN WILD-TYPE 64 28
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               22                92 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                8                28 
$`6P GAIN MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3U9 TCGA-HB-A2OT 
        2.04        27.19        42.44         6.28        14.99        26.89 
TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ 
        4.57         0.10        41.33         3.22         7.13        37.12 
TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-N1-A6IA TCGA-PC-A5DM 
      143.41         5.92         5.26         2.37         4.08         6.35 
TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-SG-A6Z7 TCGA-UE-A6QU 
       46.82        18.18         3.88         0.72 

$`6P GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 
       14.04        12.85        24.49        18.54        46.68        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       29.85        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        53.26        43.04         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75        42.77         4.54        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       28.80        34.88        64.18         9.73        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        54.87        10.78        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
        1.68        16.18         0.46         0.10         0.07         0.07 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
        4.14        12.62        23.97         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
        8.94         1.38        25.22        31.76        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        73.28        22.62         6.28         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       71.70        36.39        11.70         0.49         5.69         4.47 
TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
       11.08         0.10        75.52        37.55        38.63        81.01 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-X6-A7WB 
       18.08         1.84        18.08        21.01        13.22        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD 
       27.16         8.52 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.10              0.07 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           143.41            116.88 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            6.315            18.310 
[1] "0.1 - 143.4 (6.3)"  "0.1 - 116.9 (18.3)"
[1] "hr=" "1.7"
D11V2, continuous
D11V3, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   14  8
  6P GAIN WILD-TYPE 48 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     14    8
  6P GAIN WILD-TYPE   48   44
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              14                48
  MALE                 8                44
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       1                         2    13
  6P GAIN WILD-TYPE     3                         6    64
D11V4, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               2                 6
  WHITE                                  13                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED   14  7
  6Q GAIN WILD-TYPE 64 29
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               21                93 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                7                29 
$`6Q GAIN MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3U9 
        2.04        27.19        18.54        23.08        17.10        14.99 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ 
       26.89         4.57        41.33         3.22         7.13        37.12 
TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-N1-A6IA TCGA-PC-A5DL 
      143.41         5.92         5.26         2.37         4.08        37.55 
TCGA-PC-A5DM TCGA-QQ-A5VC TCGA-UE-A6QU 
        6.35        18.18         0.72 

$`6Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04        12.85        24.49        46.68        42.44        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       29.85        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        53.26        43.04 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
        9.04        70.49       108.13        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
       27.22        14.96        26.47        72.72        25.08        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       54.87        10.78        16.31         2.07         7.36         1.68 
TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A43Z 
       16.18         0.46         0.10         0.07         0.07         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       12.62        23.97         0.10         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
        8.94         1.38        25.22        31.76        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        73.28        22.62         6.28         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       71.70        36.39        11.70         0.49         5.69         4.47 
TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
       11.08         0.10        75.52        38.63        81.01        18.08 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT 
        1.84        46.82        18.08        21.01         3.88        13.22 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       18.08        27.16         8.52 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.72              0.07 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           143.41            116.88 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            14.99             18.08 
[1] "0.7 - 143.4 (15.0)" "0.1 - 116.9 (18.1)"
[1] "hr=" "1.4"
D12V2, continuous
D12V3, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   12  9
  6Q GAIN WILD-TYPE 50 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     12    9
  6Q GAIN WILD-TYPE   50   43
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              12                50
  MALE                 9                43
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       1                         2    14
  6Q GAIN WILD-TYPE     3                         6    63
D12V4, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               2                 6
  WHITE                                  14                63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   18 11
  7P GAIN WILD-TYPE 60 25
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               29                85 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               11                25 
$`7P GAIN MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A3LT 
       27.19        12.85        24.49        42.44        74.66        23.08 
TCGA-DX-A3U9 TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6BB TCGA-FX-A3RE TCGA-HB-A2OT 
       14.99        64.18        24.26        10.78         0.07        26.89 
TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AK 
        4.57        41.33         8.94         3.22         7.13        31.76 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-MB-A5Y9 TCGA-MO-A47R 
      143.41        13.58         5.92         1.05         2.37         0.10 
TCGA-PC-A5DL TCGA-PC-A5DP TCGA-QQ-A5V9 TCGA-SG-A6Z7 TCGA-UE-A6QU 
       37.55        18.08        46.82         3.88         0.72 

$`7P GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04         2.04        18.54        46.68        31.56        29.85 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 
        5.26        76.41        66.87         6.28        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
        8.58         9.70        53.26        43.04         9.04        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
      108.13        17.10        20.05        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
        4.54        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        19.30        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF 
       72.72        25.08        11.47        54.87        16.31         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A48G 
        7.36         1.68        16.18         0.46         0.10         0.07 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
        4.14        12.62        23.97         0.10         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K8 
       21.37         1.38        37.12        25.22        28.21       116.88 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       73.28        22.62         6.28         3.91        71.70        36.39 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       11.70         5.26         0.49         5.69         4.47        11.08 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 
        4.08        75.52         6.35        38.63        81.01         1.84 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WC 
       18.08        18.18        21.01        13.22        18.08        27.16 
TCGA-X6-A7WD 
        8.52 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.07              0.07 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           143.41            116.88 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            14.99             18.08 
[1] "0.1 - 143.4 (15.0)" "0.1 - 116.9 (18.1)"
[1] "hr=" "1.5"
D13V2, continuous
D13V3, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   19 10
  7P GAIN WILD-TYPE 43 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     19   10
  7P GAIN WILD-TYPE   43   42
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              19                43
  MALE                10                42
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       2                         2    19
  7P GAIN WILD-TYPE     2                         6    58
D13V4, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   2                 2
  BLACK OR AFRICAN AMERICAN               2                 6
  WHITE                                  19                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   17  8
  7Q GAIN WILD-TYPE 61 28
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               25                89 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                8                28 
$`7Q GAIN MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3LT 
       27.19        12.85        24.49        42.44         6.28        23.08 
TCGA-DX-A3U9 TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6BB TCGA-FX-A3RE TCGA-HB-A2OT 
       14.99        64.18        24.26        10.78         0.07        26.89 
TCGA-HB-A3YV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-IS-A3K7 
        4.57         8.94         3.22         7.13        31.76       143.41 
TCGA-IS-A3KA TCGA-JV-A5VF TCGA-MB-A5Y9 TCGA-MO-A47R TCGA-PC-A5DL TCGA-UE-A6QU 
       13.58         1.05         2.37         0.10        37.55         0.72 
TCGA-X6-A7WC 
       27.16 

$`7Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04         2.04        18.54        46.68        31.56        29.85 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
        8.58         9.70        53.26        43.04         9.04        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
      108.13        17.10        20.05        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
        4.54        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        19.30        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF 
       72.72        25.08        11.47        54.87        16.31         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A48G 
        7.36         1.68        16.18         0.46         0.10         0.07 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.14        12.62        23.97         0.10        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 
       80.48        21.37         1.38        37.12        25.22        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J 
      116.88        73.28         5.92        22.62         6.28         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JL 
       71.70        36.39        11.70         5.26         0.49         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN 
        4.47        11.08         4.08        75.52         6.35        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       81.01        18.08         1.84        46.82        18.08        18.18 
TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WD 
       21.01         3.88        13.22        18.08         8.52 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.07              0.07 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           143.41            116.88 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            13.58             18.08 
[1] "0.1 - 143.4 (13.6)" "0.1 - 116.9 (18.1)"
[1] "hr=" "1.3"
D14V2, continuous
D14V3, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   14 11
  7Q GAIN WILD-TYPE 48 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     14   11
  7Q GAIN WILD-TYPE   48   41
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              14                48
  MALE                11                41
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       2                         2    16
  7Q GAIN WILD-TYPE     2                         6    61
D14V4, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   2                 2
  BLACK OR AFRICAN AMERICAN               2                 6
  WHITE                                  16                61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   13 12
  8P GAIN WILD-TYPE 65 24
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               25                89 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12                24 
$`8P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UF 
       14.04        12.85        74.66         4.54        14.99        64.18 
TCGA-DX-A6BA TCGA-FX-A3NJ TCGA-HB-A3YV TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
       54.87         0.10         4.57        80.48         8.94         3.22 
TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-MJ-A68H 
       31.76        13.58         5.92         1.05         3.91         4.47 
TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM TCGA-UE-A6QT 
       11.08         0.10         4.08        37.55         6.35        13.22 
TCGA-UE-A6QU 
        0.72 

$`8P GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        27.19        24.49        18.54        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       31.56        29.85         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        53.26        43.04 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       15.06        17.75        42.77        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       28.80        34.88         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
       27.22        14.96        26.47        72.72        25.08        11.47 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       10.78        16.31         2.07         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 
        0.46         0.07         0.07        26.89         4.14        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EK 
       23.97         0.10        41.33         9.80        21.37         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        7.13        37.12        25.22        28.21       143.41       116.88 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W 
       73.28        22.62         6.28        71.70        36.39        11.70 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-PC-A5DK TCGA-PC-A5DN 
        5.26         2.37         0.49         5.69        75.52        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       81.01        18.08         1.84        46.82        18.08        18.18 
TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       21.01         3.88        18.08        27.16         8.52 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.10              0.07 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            80.48            143.41 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             8.94             20.05 
[1] "0.1 - 80.5 (8.9)"   "0.1 - 143.4 (20.1)"
[1] "hr=" "2.8"
D15V2, continuous
D15V3, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   16  9
  8P GAIN WILD-TYPE 46 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     16    9
  8P GAIN WILD-TYPE   46   43
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              16                46
  MALE                 9                43
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       3                         4    15
  8P GAIN WILD-TYPE     1                         4    62
D15V4, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   3                 1
  BLACK OR AFRICAN AMERICAN               4                 4
  WHITE                                  15                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   15 14
  8Q GAIN WILD-TYPE 63 22
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               29                85 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               14                22 
$`8Q GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       14.04        12.85        74.66        42.77         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A6BA TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-HB-A3YV 
       10.68        64.18        54.87         0.46         0.10         4.57 
TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA 
       41.33        80.48         8.94        25.22        31.76        13.58 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
        5.92         1.05         3.91         4.47        11.08         0.10 
TCGA-N1-A6IA TCGA-PC-A5DL TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU 
        4.08        37.55         3.88        13.22         0.72 

$`8Q GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        27.19        24.49        18.54        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       31.56        29.85         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        53.26        43.04 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       15.06        17.75        44.45        39.35        28.80        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        19.30        24.26        12.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       26.47        72.72        25.08        11.47        10.78        16.31 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A3RE TCGA-FX-A48G 
        2.07         7.36         1.68        16.18         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
       26.89         4.14        12.62        23.97         0.10         9.80 
TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 
       21.37         3.22         1.38         7.13        37.12        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN 
      143.41       116.88        73.28        22.62         6.28        71.70 
TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       36.39        11.70         5.26         2.37         0.49         5.69 
TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 
       75.52         6.35        38.63        81.01        18.08         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-X6-A7WB TCGA-X6-A7WC 
       46.82        18.08        18.18        21.01        18.08        27.16 
TCGA-X6-A7WD 
        8.52 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.10              0.07 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            80.48            143.41 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            11.08             19.30 
[1] "0.1 - 80.5 (11.1)"  "0.1 - 143.4 (19.3)"
[1] "hr=" "2.7"
D16V2, continuous
D16V3, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   19 10
  8Q GAIN WILD-TYPE 43 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     19   10
  8Q GAIN WILD-TYPE   43   42
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              19                43
  MALE                10                42
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       3                         4    18
  8Q GAIN WILD-TYPE     1                         4    59
D16V4, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   3                 1
  BLACK OR AFRICAN AMERICAN               4                 4
  WHITE                                  18                59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED   11  8
  9P GAIN WILD-TYPE 67 28
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               19                95 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                8                28 
$`9P GAIN MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A3LU TCGA-DX-A3U9 
        2.04        27.19        24.49        42.44        70.49        14.99 
TCGA-DX-A3UA TCGA-DX-A48N TCGA-DX-A6BB TCGA-DX-A6BK TCGA-IE-A6BZ TCGA-IF-A4AK 
       10.68        12.26        10.78        16.18         7.13        31.76 
TCGA-IS-A3KA TCGA-JV-A5VF TCGA-KF-A41W TCGA-LI-A67I TCGA-PC-A5DP TCGA-QQ-A5V9 
       13.58         1.05        11.70         5.26        18.08        46.82 
TCGA-SG-A6Z7 
        3.88 

$`9P GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04        12.85        18.54        46.68        31.56        29.85 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       74.66         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        53.26        43.04         9.04 
TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       23.08       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       42.77         4.54        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       64.18         9.73        19.30        24.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE 
       26.47        72.72        25.08        11.47        54.87        16.31 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
        2.07         7.36         1.68         0.46         0.10         0.07 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07        26.89         4.57         4.14        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
        0.10        41.33         9.80        80.48        21.37         8.94 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 
        3.22         1.38        37.12        25.22        28.21       143.41 
TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J 
      116.88        73.28         5.92        22.62         6.28         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       71.70        36.39         2.37         0.49         5.69         4.47 
TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
       11.08         0.10         4.08        75.52        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
       38.63        81.01         1.84        18.08        18.18        21.01 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       13.22         0.72        18.08        27.16         8.52 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.05              0.07 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            70.49            143.41 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            13.58             18.18 
[1] "1.1 - 70.5 (13.6)"  "0.1 - 143.4 (18.2)"
[1] "hr=" "1.9"
D17V2, continuous
D17V3, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   11  8
  9P GAIN WILD-TYPE 51 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     11    8
  9P GAIN WILD-TYPE   51   44
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              11                51
  MALE                 8                44
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       0                         1    14
  9P GAIN WILD-TYPE     4                         7    63
D17V4, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               1                 7
  WHITE                                  14                63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED   20  6
  9Q GAIN WILD-TYPE 58 30
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               26                88 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                6                30 
$`9Q GAIN MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23R 
        2.04        27.19        24.49        46.68        42.44        74.66 
TCGA-DX-A3LU TCGA-DX-A3M1 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A6BA 
       70.49        20.05        42.77        14.99        10.68        54.87 
TCGA-DX-A6BB TCGA-DX-A6BK TCGA-FX-A2QS TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ 
       10.78        16.18         0.46         8.94         3.22         7.13 
TCGA-IF-A4AK TCGA-JV-A5VF TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-PC-A5DP 
       31.76         1.05        11.70         5.26         2.37        18.08 
TCGA-QQ-A5V9 TCGA-QQ-A5VC 
       46.82        18.18 

$`9Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       14.04        12.85        18.54        31.56        29.85         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW 
        9.70        53.26        43.04         9.04        23.08       108.13 
TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC 
       17.10        15.06        17.75         4.54        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       28.80        34.88        64.18         9.73        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A3NJ 
       11.47        16.31         2.07         7.36         1.68         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        0.07         0.07        26.89         4.57         4.14        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       23.97         0.10        41.33         9.80        80.48        21.37 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        1.38        37.12        25.22        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J 
       13.58        73.28         5.92        22.62         6.28         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       71.70        36.39         0.49         5.69         4.47        11.08 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
        0.10         4.08        75.52        37.55         6.35        38.63 
TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT 
       81.01         1.84        18.08        21.01         3.88        13.22 
TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        0.72        18.08        27.16         8.52 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.46              0.07 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            74.66            143.41 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           17.130            17.915 
[1] "0.5 - 74.7 (17.1)"  "0.1 - 143.4 (17.9)"
[1] "hr=" "1.3"
D18V2, continuous
D18V3, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   15 11
  9Q GAIN WILD-TYPE 47 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     15   11
  9Q GAIN WILD-TYPE   47   41
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              15                47
  MALE                11                41
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       0                         1    19
  9Q GAIN WILD-TYPE     4                         7    58
D18V4, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               1                 7
  WHITE                                  19                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    5  5
  10P GAIN WILD-TYPE 73 31
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                10                104 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 5                 31 
$`10P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-HS-A5N9 TCGA-IE-A6BZ 
       14.04        23.08        42.77         4.54        41.33         7.13 
TCGA-IS-A3KA TCGA-JV-A5VF TCGA-LI-A67I TCGA-QQ-A5VA 
       13.58         1.05         5.26        18.08 

$`10P GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
        2.04        27.19        12.85        24.49        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       42.44        31.56        29.85        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       53.26        43.04         9.04        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       20.05        15.06        17.75        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       25.08        11.47        54.87        10.78        16.31         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
        7.36         1.68        16.18         0.46         0.10         0.07 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07        26.89         4.57         4.14        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
        0.10         9.80        80.48        21.37         8.94         3.22 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        1.38        37.12        25.22        31.76        28.21       143.41 
TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J 
      116.88        73.28         5.92        22.62         6.28         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       71.70        36.39        11.70         2.37         0.49         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
        4.47        11.08         0.10         4.08        75.52        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 
        6.35        38.63        81.01        18.08         1.84        46.82 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB 
       18.18        21.01         3.88        13.22         0.72        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD 
       27.16         8.52 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1.05               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             42.77             143.41 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             13.81              18.08 
[1] "1.1 - 42.8 (13.8)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "2.4"
D19V2, continuous
D19V3, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    6  4
  10P GAIN WILD-TYPE 56 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      6    4
  10P GAIN WILD-TYPE   56   48
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                6                 56
  MALE                  4                 48
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       0                         1     7
  10P GAIN WILD-TYPE     4                         7    70
D19V4, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                1                  7
  WHITE                                    7                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED    1  3
  10Q GAIN WILD-TYPE 77 33
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                110 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                 33 
$`10Q GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A3LT TCGA-DX-A3U8 TCGA-SG-A6Z7 
       14.04        23.08         4.54         3.88 

$`10Q GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
        2.04        27.19        12.85        24.49        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       42.44        31.56        29.85        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       53.26        43.04         9.04        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA 
       20.05        15.06        17.75        42.77        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       19.30        24.26        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       72.72        25.08        11.47        54.87        10.78        16.31 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ 
        2.07         7.36         1.68        16.18         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        0.07         0.07        26.89         4.57         4.14        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       23.97         0.10        41.33         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
        8.94         3.22         1.38         7.13        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       31.76        28.21       143.41       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
        5.92        22.62         6.28         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       36.39        11.70         5.26         2.37         0.49         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
        4.47        11.08         0.10         4.08        75.52        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 
        6.35        38.63        81.01        18.08         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB 
       18.08        18.18        21.01        13.22         0.72        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD 
       27.16         8.52 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              3.88               0.07 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             23.08             143.41 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              9.29              18.08 
[1] "3.9 - 23.1 (9.3)"   "0.1 - 143.4 (18.1)"
[1] "hr=" "5.8"
D20V2, continuous
D20V3, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    1  3
  10Q GAIN WILD-TYPE 61 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    3
  10Q GAIN WILD-TYPE   61   49
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                1                 61
  MALE                  3                 49
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         0     3
  10Q GAIN WILD-TYPE     4                         8    74
D20V4, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                0                  8
  WHITE                                    3                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    2  4
  11P GAIN WILD-TYPE 76 32
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                108 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                 32 
$`11P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A6BK TCGA-IE-A4EJ TCGA-IS-A3KA TCGA-KF-A41W TCGA-PC-A5DP 
       14.04        16.18         3.22        13.58        11.70        18.08 

$`11P GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
        2.04        27.19        12.85        24.49        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       42.44        31.56        29.85        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       53.26        43.04         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       17.10        20.05        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       64.18         9.73        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        26.47        72.72        25.08        11.47        54.87 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS 
       10.78        16.31         2.07         7.36         1.68         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z 
        0.10         0.07         0.07        26.89         4.57         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       12.62        23.97         0.10        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
       21.37         8.94         1.38         7.13        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 
       31.76        28.21       143.41       116.88        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       22.62         6.28         1.05         3.91        71.70        36.39 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        5.26         2.37         0.49         5.69         4.47        11.08 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
        0.10         4.08        75.52        37.55         6.35        38.63 
TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
       81.01         1.84        46.82        18.08        18.18        21.01 
TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        3.88        13.22         0.72        18.08        27.16         8.52 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              3.22               0.07 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             18.08             143.41 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             13.81              18.13 
[1] "3.2 - 18.1 (13.8)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "4.4"
D21V2, continuous
D21V3, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    5  1
  11P GAIN WILD-TYPE 57 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5    1
  11P GAIN WILD-TYPE   57   51
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                5                 57
  MALE                  1                 51
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         0     6
  11P GAIN WILD-TYPE     4                         8    71
D21V4, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                0                  8
  WHITE                                    6                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    3  2
  11Q GAIN WILD-TYPE 75 34
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                109 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 34 
$`11Q GAIN MUTATED`
TCGA-DX-A1KU TCGA-HB-A43Z TCGA-IE-A4EH TCGA-KF-A41W TCGA-PC-A5DP 
       14.04         4.14        21.37        11.70        18.08 

$`11Q GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
        2.04        27.19        12.85        24.49        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       42.44        31.56        29.85        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       53.26        43.04         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       17.10        20.05        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       64.18         9.73        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        26.47        72.72        25.08        11.47        54.87 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       10.78        16.31         2.07         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV 
        0.46         0.10         0.07         0.07        26.89         4.57 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       12.62        23.97         0.10        41.33         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
        8.94         3.22         1.38         7.13        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       31.76        28.21       143.41       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
        5.92        22.62         6.28         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       36.39         5.26         2.37         0.49         5.69         4.47 
TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
       11.08         0.10         4.08        75.52        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       38.63        81.01         1.84        46.82        18.08        18.18 
TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC 
       21.01         3.88        13.22         0.72        18.08        27.16 
TCGA-X6-A7WD 
        8.52 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              4.14               0.07 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             21.37             143.41 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             14.04              18.08 
[1] "4.1 - 21.4 (14.0)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "2.2"
D22V2, continuous
D22V3, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    4  1
  11Q GAIN WILD-TYPE 58 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4    1
  11Q GAIN WILD-TYPE   58   51
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                4                 58
  MALE                  1                 51
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         0     5
  11Q GAIN WILD-TYPE     4                         8    72
D22V4, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                0                  8
  WHITE                                    5                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    5  8
  12P GAIN WILD-TYPE 73 28
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                13                101 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 8                 28 
$`12P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A3LS TCGA-HB-A3YV TCGA-HS-A5N8 
       14.04        27.19        12.85         9.04         4.57         0.10 
TCGA-IF-A4AJ TCGA-IW-A3M5 TCGA-MB-A5Y9 TCGA-MO-A47R TCGA-PC-A5DL TCGA-QQ-A5VA 
       25.22         5.92         2.37         0.10        37.55        18.08 
TCGA-UE-A6QU 
        0.72 

$`12P GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
        2.04        24.49        18.54        46.68        42.44        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       29.85        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        53.26        43.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       25.08        11.47        54.87        10.78        16.31         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
        7.36         1.68        16.18         0.46         0.10         0.07 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 
        0.07        26.89         4.14        12.62        23.97        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37         8.94         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        7.13        37.12        31.76        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        73.28        22.62         6.28         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JL 
       71.70        36.39        11.70         5.26         0.49         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN 
        4.47        11.08         4.08        75.52         6.35        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD 
       81.01        18.08         1.84        46.82        18.18        21.01 
TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        3.88        13.22        18.08        27.16         8.52 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.10               0.07 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             37.55             143.41 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              9.04              18.18 
[1] "0.1 - 37.5 (9.0)"   "0.1 - 143.4 (18.2)"
[1] "hr=" "4.8"
D23V2, continuous
D23V3, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    7  6
  12P GAIN WILD-TYPE 55 46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      7    6
  12P GAIN WILD-TYPE   55   46
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                7                 55
  MALE                  6                 46
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       2                         0     8
  12P GAIN WILD-TYPE     2                         8    69
D23V4, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    2                  2
  BLACK OR AFRICAN AMERICAN                0                  8
  WHITE                                    8                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    5  3
  12Q GAIN WILD-TYPE 73 33
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 8                106 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 33 
$`12Q GAIN MUTATED`
TCGA-DX-A1KX TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IF-A4AJ TCGA-MO-A47R 
       27.19         4.57         0.10        41.33        25.22         0.10 
TCGA-PC-A5DL TCGA-UE-A6QU 
       37.55         0.72 

$`12Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        12.85        24.49        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       42.44        31.56        29.85        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       53.26        43.04         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       17.10        20.05        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       64.18         9.73        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        26.47        72.72        25.08        11.47        54.87 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       10.78        16.31         2.07         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A43Z 
        0.46         0.10         0.07         0.07        26.89         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
       12.62        23.97         9.80        80.48        21.37         8.94 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 
        3.22         1.38         7.13        37.12        31.76        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
      143.41       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W 
        6.28         1.05         3.91        71.70        36.39        11.70 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        5.26         2.37         0.49         5.69         4.47        11.08 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
        4.08        75.52         6.35        38.63        81.01        18.08 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 
        1.84        46.82        18.08        18.18        21.01         3.88 
TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       13.22        18.08        27.16         8.52 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.10               0.07 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             41.33             143.41 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            14.895             17.915 
[1] "0.1 - 41.3 (14.9)"  "0.1 - 143.4 (17.9)"
[1] "hr=" "1.7"
D24V2, continuous
D24V3, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    5  3
  12Q GAIN WILD-TYPE 57 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      5    3
  12Q GAIN WILD-TYPE   57   49
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                5                 57
  MALE                  3                 49
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       2                         0     3
  12Q GAIN WILD-TYPE     2                         8    74
D24V4, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    2                  2
  BLACK OR AFRICAN AMERICAN                0                  8
  WHITE                                    3                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    4  2
  13Q GAIN WILD-TYPE 74 34
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                108 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                 34 
$`13Q GAIN MUTATED`
TCGA-DX-A3U9 TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-JV-A5VE TCGA-MJ-A68H TCGA-PC-A5DP 
       14.99        41.33        31.76         6.28         4.47        18.08 

$`13Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        42.44        31.56        29.85        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        53.26        43.04         9.04        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
      108.13        17.10        20.05        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
        4.54        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       64.18         9.73        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        26.47        72.72        25.08        11.47        54.87 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       10.78        16.31         2.07         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV 
        0.46         0.10         0.07         0.07        26.89         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
        4.14        12.62        23.97         0.10         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       21.37         8.94         3.22         1.38         7.13        37.12 
TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       25.22        28.21       143.41       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        22.62         1.05         3.91        71.70        36.39 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J 
       11.70         5.26         2.37         0.49         5.69        11.08 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
        0.10         4.08        75.52        37.55         6.35        38.63 
TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
       81.01         1.84        46.82        18.08        18.18        21.01 
TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        3.88        13.22         0.72        18.08        27.16         8.52 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              4.47               0.07 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             41.33             143.41 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            16.535             17.915 
[1] "4.5 - 41.3 (16.5)"  "0.1 - 143.4 (17.9)"
[1] "hr=" "1.3"
D25V2, continuous
D25V3, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    5  1
  13Q GAIN WILD-TYPE 57 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5    1
  13Q GAIN WILD-TYPE   57   51
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                5                 57
  MALE                  1                 51
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       0                         2     3
  13Q GAIN WILD-TYPE     4                         6    74
D25V4, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                2                  6
  WHITE                                    3                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED   10 11
  14Q GAIN WILD-TYPE 68 25
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                21                 93 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                 25 
$`14Q GAIN MUTATED`
TCGA-DX-A1L1 TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A3LW TCGA-DX-A3U9 TCGA-DX-A3UF 
       46.68         6.28        60.30       108.13        14.99        64.18 
TCGA-DX-A48L TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA 
       24.26         4.57        12.62        25.22        31.76        13.58 
TCGA-IW-A3M5 TCGA-KF-A41W TCGA-MB-A8JL TCGA-MJ-A68H TCGA-PC-A5DM TCGA-PC-A5DP 
        5.92        11.70         5.69         4.47         6.35        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 
       18.18        21.01         3.88 

$`14Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       42.44        31.56        29.85        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       66.87        27.81         8.58         9.70        53.26        43.04 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
        9.04        23.08        70.49        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75        42.77         4.54        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       28.80        34.88         9.73        19.30        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        26.47        72.72        25.08        11.47        54.87 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       10.78        16.31         2.07         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A43Z 
        0.46         0.10         0.07         0.07        26.89         4.14 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       23.97         0.10        41.33         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 
        8.94         3.22         1.38         7.13        37.12        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
      143.41       116.88        73.28        22.62         6.28         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA 
        3.91        71.70        36.39         5.26         2.37         0.49 
TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.08         0.10         4.08        75.52        37.55        38.63 
TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-UE-A6QT TCGA-UE-A6QU 
       81.01         1.84        46.82        18.08        13.22         0.72 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       18.08        27.16         8.52 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              3.88               0.07 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            108.13             143.41 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             14.99              18.08 
[1] "3.9 - 108.1 (15.0)" "0.1 - 143.4 (18.1)"
[1] "hr=" "2.1"
D26V2, continuous
D26V3, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   12  9
  14Q GAIN WILD-TYPE 50 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     12    9
  14Q GAIN WILD-TYPE   50   43
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               12                 50
  MALE                  9                 43
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         1    17
  14Q GAIN WILD-TYPE     4                         7    60
D26V4, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                1                  7
  WHITE                                   17                 60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED   17 12
  15Q GAIN WILD-TYPE 61 24
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                29                 85 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                12                 24 
$`15Q GAIN MUTATED`
TCGA-DX-A1L4 TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC 
       29.85         6.28         8.58        42.77        14.99        39.35 
TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6BA TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 
       64.18        24.26        54.87         4.14        12.62        41.33 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA 
        8.94         3.22         7.13        25.22        31.76        13.58 
TCGA-JV-A75J TCGA-LI-A67I TCGA-MJ-A68H TCGA-PC-A5DL TCGA-PC-A5DP TCGA-QQ-A5V9 
        3.91         5.26         4.47        37.55        18.08        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QU 
       18.08        18.18        21.01         3.88         0.72 

$`15Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       46.68        42.44        31.56        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       66.87        27.81        60.30         9.70        53.26        43.04 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD 
       15.06        17.75         4.54        10.68        44.45        28.80 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       34.88         9.73        19.30        12.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       26.47        72.72        25.08        11.47        10.78        16.31 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ 
        2.07         7.36         1.68        16.18         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 
        0.07         0.07        26.89         4.57        23.97         0.10 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K6 
        9.80        80.48        21.37         1.38        37.12        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      143.41       116.88        73.28         5.92        22.62         6.28 
TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A5YA 
        1.05        71.70        36.39        11.70         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM 
        5.69        11.08         0.10         4.08        75.52         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WC 
       38.63        81.01         1.84        13.22        18.08        27.16 
TCGA-X6-A7WD 
        8.52 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.72               0.07 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             64.18             143.41 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             18.08              17.75 
[1] "0.7 - 64.2 (18.1)"  "0.1 - 143.4 (17.8)"
[1] "hr=" "1.8"
D27V2, continuous
D27V3, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   20  9
  15Q GAIN WILD-TYPE 42 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     20    9
  15Q GAIN WILD-TYPE   42   43
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               20                 42
  MALE                  9                 43
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       1                         1    23
  15Q GAIN WILD-TYPE     3                         7    54
D27V4, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                1                  7
  WHITE                                   23                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    8  9
  16P GAIN WILD-TYPE 70 27
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                17                 97 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 9                 27 
$`16P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A2J0 TCGA-DX-A3U5 TCGA-DX-A3U9 
       14.04         2.04        27.19         9.70        15.06        14.99 
TCGA-DX-A48L TCGA-FX-A2QS TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IF-A4AJ TCGA-IF-A4AK 
       24.26         0.46        80.48        21.37        25.22        31.76 
TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-LI-A67I TCGA-MO-A47R TCGA-SG-A6Z7 
       13.58         5.92         5.26         0.10         3.88 

$`16P GAIN WILD-TYPE`
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       12.85        24.49        18.54        46.68        42.44        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       29.85        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         8.58        53.26        43.04         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U6 
       23.08        70.49       108.13        17.10        20.05        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       34.88        64.18         9.73        19.30        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        26.47        72.72        25.08        11.47        54.87 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       10.78        16.31         2.07         7.36         1.68        16.18 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z 
        0.10         0.07         0.07        26.89         4.57         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EI 
       12.62        23.97         0.10        41.33         9.80         8.94 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 
        3.22         1.38         7.13        37.12        28.21       143.41 
TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
      116.88        73.28        22.62         6.28         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       71.70        36.39        11.70         2.37         0.49         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
        4.47        11.08         4.08        75.52        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       38.63        81.01        18.08         1.84        46.82        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC 
       18.18        21.01        13.22         0.72        18.08        27.16 
TCGA-X6-A7WD 
        8.52 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.10               0.07 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             80.48             143.41 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             14.04              18.08 
[1] "0.1 - 80.5 (14.0)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "2.8"
D28V2, continuous
D28V3, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   10  7
  16P GAIN WILD-TYPE 52 45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     10    7
  16P GAIN WILD-TYPE   52   45
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               10                 52
  MALE                  7                 45
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       1                         0    13
  16P GAIN WILD-TYPE     3                         8    64
D28V4, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                0                  8
  WHITE                                   13                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    3  3
  16Q GAIN WILD-TYPE 75 33
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                108 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 33 
$`16Q GAIN MUTATED`
TCGA-DX-A1KW TCGA-DX-A3U5 TCGA-IE-A3OV TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-SG-A6Z7 
        2.04        15.06        80.48       143.41         5.92         3.88 

$`16Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04        27.19        12.85        24.49        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       42.44        31.56        29.85        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       53.26        43.04         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       17.10        20.05        17.75        42.77         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        44.45        39.35        28.80        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        19.30        24.26        12.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       26.47        72.72        25.08        11.47        54.87        10.78 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS 
       16.31         2.07         7.36         1.68        16.18         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z 
        0.10         0.07         0.07        26.89         4.57         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH 
       12.62        23.97         0.10        41.33         9.80        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
        8.94         3.22         1.38         7.13        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 
       31.76        28.21       116.88        13.58        73.28        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W 
        6.28         1.05         3.91        71.70        36.39        11.70 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        5.26         2.37         0.49         5.69         4.47        11.08 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
        0.10         4.08        75.52        37.55         6.35        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       81.01        18.08         1.84        46.82        18.08        18.18 
TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       21.01        13.22         0.72        18.08        27.16         8.52 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              2.04               0.07 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            143.41             116.88 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             10.49              18.08 
[1] "2.0 - 143.4 (10.5)" "0.1 - 116.9 (18.1)"
[1] "hr=" "1.1"
D29V2, continuous
D29V3, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3  3
  16Q GAIN WILD-TYPE 59 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    3
  16Q GAIN WILD-TYPE   59   49
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                3                 59
  MALE                  3                 49
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       0                         0     5
  16Q GAIN WILD-TYPE     4                         8    72
D29V4, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                0                  8
  WHITE                                    5                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED   14  8
  17P GAIN WILD-TYPE 64 28
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                22                 92 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                 28 
$`17P GAIN MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3UF 
        2.04        12.85        46.68        42.44         6.28        64.18 
TCGA-DX-A48K TCGA-DX-A48R TCGA-DX-A6BF TCGA-DX-A6BK TCGA-FX-A3RE TCGA-FX-A48G 
       19.30        26.47         2.07        16.18         0.07         0.07 
TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-JV-A75J TCGA-LI-A67I TCGA-MO-A47R TCGA-N1-A6IA 
        4.57        12.62         3.91         5.26         0.10         4.08 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-UE-A6QU TCGA-X6-A7WC 
       46.82        18.08         0.72        27.16 

$`17P GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04        27.19        24.49        18.54        31.56        29.85 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        53.26        43.04         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       42.77         4.54        14.99        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       28.80        34.88         9.73        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       14.96        72.72        25.08        11.47        54.87        10.78 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-HB-A2OT 
       16.31         7.36         1.68         0.46         0.10        26.89 
TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
        4.14        23.97         0.10        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       21.37         8.94         3.22         1.38         7.13        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        31.76        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN 
       73.28         5.92        22.62         6.28         1.05        71.70 
TCGA-K1-A3PO TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       36.39        11.70         2.37         0.49         5.69         4.47 
TCGA-MJ-A68J TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
       11.08        75.52        37.55         6.35        38.63        81.01 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT 
       18.08         1.84        18.18        21.01         3.88        13.22 
TCGA-X6-A7WB TCGA-X6-A7WD 
       18.08         8.52 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.07               0.10 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             64.18             143.41 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              9.45              18.36 
[1] "0.1 - 64.2 (9.4)"   "0.1 - 143.4 (18.4)"
[1] "hr=" "2"  
D30V2, continuous
D30V3, binary
                    cls
clus                  0  1
  17P GAIN MUTATED   12 10
  17P GAIN WILD-TYPE 50 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     12   10
  17P GAIN WILD-TYPE   50   42
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               12                 50
  MALE                 10                 42
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       2                         1    14
  17P GAIN WILD-TYPE     2                         7    63
D30V4, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    2                  2
  BLACK OR AFRICAN AMERICAN                1                  7
  WHITE                                   14                 63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED   12  4
  17Q GAIN WILD-TYPE 66 32
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                16                 98 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 4                 32 
$`17Q GAIN MUTATED`
TCGA-DX-A1KW TCGA-DX-A1L2 TCGA-DX-A48K TCGA-DX-A6BF TCGA-DX-A6BK TCGA-FX-A3RE 
        2.04        42.44        19.30         2.07        16.18         0.07 
TCGA-FX-A48G TCGA-HB-A5W3 TCGA-IE-A6BZ TCGA-IW-A3M4 TCGA-JV-A75J TCGA-LI-A67I 
        0.07        12.62         7.13        73.28         3.91         5.26 
TCGA-MO-A47R TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-UE-A6QU 
        0.10        18.08        18.18         0.72 

$`17Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04        27.19        12.85        24.49        18.54        46.68 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        29.85        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       43.04         9.04        23.08        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       20.05        15.06        17.75        42.77         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        44.45        39.35        28.80        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        24.26        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       72.72        25.08        11.47        54.87        10.78        16.31 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-HB-A2OT TCGA-HB-A3YV 
        7.36         1.68         0.46         0.10        26.89         4.57 
TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
        4.14        23.97         0.10        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
       21.37         8.94         3.22         1.38        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M5 
       31.76        28.21       143.41       116.88        13.58         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W 
       22.62         6.28         1.05        71.70        36.39        11.70 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-N1-A6IA 
        2.37         0.49         5.69         4.47        11.08         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
       75.52        37.55         6.35        38.63        81.01        18.08 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WB 
        1.84        46.82        21.01         3.88        13.22        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD 
       27.16         8.52 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.07               0.10 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             73.28             143.41 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             6.195             19.295 
[1] "0.1 - 73.3 (6.2)"   "0.1 - 143.4 (19.3)"
[1] "hr=" "1.5"
D31V2, continuous
D31V3, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   13  3
  17Q GAIN WILD-TYPE 49 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     13    3
  17Q GAIN WILD-TYPE   49   49
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               13                 49
  MALE                  3                 49
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       2                         0    12
  17Q GAIN WILD-TYPE     2                         8    65
D31V4, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    2                  2
  BLACK OR AFRICAN AMERICAN                0                  8
  WHITE                                   12                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED   12  5
  18P GAIN WILD-TYPE 66 31
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                17                 97 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                 31 
$`18P GAIN MUTATED`
TCGA-DX-A1KW TCGA-DX-A1L3 TCGA-DX-A3U7 TCGA-DX-A3UE TCGA-DX-A6BA TCGA-HB-A43Z 
        2.04        31.56        42.77        34.88        54.87         4.14 
TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE 
        0.10         8.94         7.13        13.58         5.92         6.28 
TCGA-MB-A5Y9 TCGA-MO-A47R TCGA-PC-A5DM TCGA-QQ-A5V9 TCGA-X6-A7WC 
        2.37         0.10         6.35        46.82        27.16 

$`18P GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04        27.19        12.85        24.49        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       42.44        29.85        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       43.04         9.04        23.08        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       20.05        15.06        17.75         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       44.45        39.35        28.80        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       25.08        11.47        10.78        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
        1.68        16.18         0.46         0.10         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA 
       26.89         4.57        12.62        23.97        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
       80.48        21.37         3.22         1.38        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 
       31.76        28.21       143.41       116.88        73.28        22.62 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I 
        1.05         3.91        71.70        36.39        11.70         5.26 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-N1-A6IA TCGA-PC-A5DK 
        0.49         5.69         4.47        11.08         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA 
       37.55        38.63        81.01        18.08         1.84        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB 
       18.18        21.01         3.88        13.22         0.72        18.08 
TCGA-X6-A7WD 
        8.52 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.10               0.07 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             54.87             143.41 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              7.13              18.08 
[1] "0.1 - 54.9 (7.1)"   "0.1 - 143.4 (18.1)"
[1] "hr=" "1.4"
D32V2, continuous
D32V3, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   11  6
  18P GAIN WILD-TYPE 51 46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     11    6
  18P GAIN WILD-TYPE   51   46
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               11                 51
  MALE                  6                 46
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       1                         1    12
  18P GAIN WILD-TYPE     3                         7    65
D32V4, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                1                  7
  WHITE                                   12                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED   11  5
  18Q GAIN WILD-TYPE 67 31
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                16                 98 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                 31 
$`18Q GAIN MUTATED`
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A3U7 TCGA-DX-A3UE TCGA-FX-A2QS TCGA-HB-A43Z 
       42.44        31.56        42.77        34.88         0.46         4.14 
TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE 
        0.10         8.94         7.13        13.58         5.92         6.28 
TCGA-MB-A5Y9 TCGA-MO-A47R TCGA-PC-A5DL TCGA-QQ-A5V9 
        2.37         0.10        37.55        46.82 

$`18Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       46.68        29.85        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       43.04         9.04        23.08        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       20.05        15.06        17.75         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       44.45        39.35        28.80        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       25.08        11.47        54.87        10.78        16.31         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
        7.36         1.68        16.18         0.10         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA 
       26.89         4.57        12.62        23.97        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
       80.48        21.37         3.22         1.38        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 
       31.76        28.21       143.41       116.88        73.28        22.62 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I 
        1.05         3.91        71.70        36.39        11.70         5.26 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-N1-A6IA TCGA-PC-A5DK 
        0.49         5.69         4.47        11.08         4.08        75.52 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA 
        6.35        38.63        81.01        18.08         1.84        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB 
       18.18        21.01         3.88        13.22         0.72        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD 
       27.16         8.52 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.10               0.07 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             46.82             143.41 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             8.035             18.080 
[1] "0.1 - 46.8 (8.0)"   "0.1 - 143.4 (18.1)"
[1] "hr=" "1.4"
D33V2, continuous
D33V3, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED   11  5
  18Q GAIN WILD-TYPE 51 47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     11    5
  18Q GAIN WILD-TYPE   51   47
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               11                 51
  MALE                  5                 47
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       1                         1    11
  18Q GAIN WILD-TYPE     3                         7    66
D33V4, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                1                  7
  WHITE                                   11                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED   19 14
  19P GAIN WILD-TYPE 59 22
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                33                 81 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                14                 22 
$`19P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        27.19        12.85        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3U7 TCGA-DX-A3U9 
       42.44        74.66         6.28         9.70        42.77        14.99 
TCGA-DX-A3UF TCGA-DX-A48N TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV TCGA-HS-A5NA 
       64.18        12.26         0.07         0.07         4.57         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IW-A3M5 TCGA-JV-A5VF 
       80.48         8.94         3.22         7.13         5.92         1.05 
TCGA-JV-A75J TCGA-KF-A41W TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-UE-A6QT 
        3.91        11.70        46.82        18.08        18.18        13.22 
TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC 
        0.72        18.08        27.16 

$`19P GAIN WILD-TYPE`
TCGA-DX-A1KZ TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       24.49        31.56        29.85         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         8.58        53.26        43.04         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       17.75         4.54        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       34.88         9.73        19.30        24.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       26.47        72.72        25.08        11.47        54.87        10.78 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS 
       16.31         2.07         7.36         1.68        16.18         0.46 
TCGA-FX-A3NJ TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
        0.10        26.89         4.14        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK 
       41.33        21.37         1.38        37.12        25.22        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 
       28.21       143.41       116.88        13.58        73.28        22.62 
TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA 
        6.28        71.70        36.39         5.26         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
        5.69         4.47        11.08         0.10         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 
       37.55         6.35        38.63        81.01        18.08         1.84 
TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-X6-A7WD 
       21.01         3.88         8.52 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.07               0.10 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             80.48             143.41 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             12.85              21.01 
[1] "0.1 - 80.5 (12.8)"  "0.1 - 143.4 (21.0)"
[1] "hr=" "2.1"
D34V2, continuous
D34V3, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   18 15
  19P GAIN WILD-TYPE 44 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     18   15
  19P GAIN WILD-TYPE   44   37
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               18                 44
  MALE                 15                 37
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       2                         1    20
  19P GAIN WILD-TYPE     2                         7    57
D34V4, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    2                  2
  BLACK OR AFRICAN AMERICAN                1                  7
  WHITE                                   20                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   16  6
  19Q GAIN WILD-TYPE 62 30
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                22                 92 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                 30 
$`19Q GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04         2.04        27.19        12.85        46.68        42.44 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3U9 TCGA-DX-A3UF TCGA-DX-A48N TCGA-HS-A5NA 
       74.66         6.28        14.99        64.18        12.26         9.80 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-JV-A5VF TCGA-KF-A41W TCGA-MJ-A68H 
        8.94         3.22         7.13         1.05        11.70         4.47 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-UE-A6QU TCGA-X6-A7WC 
       18.08        18.18         0.72        27.16 

$`19Q GAIN WILD-TYPE`
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       24.49        18.54        31.56        29.85         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87        27.81        60.30         8.58         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       43.04         9.04        23.08        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
       20.05        15.06        17.75        42.77         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       44.45        39.35        28.80        34.88         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       24.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        54.87        10.78        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
        1.68        16.18         0.46         0.10         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       26.89         4.57         4.14        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
       41.33        80.48        21.37         1.38        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       31.76        28.21       143.41       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        22.62         6.28         3.91        71.70        36.39 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MO-A47R 
        5.26         2.37         0.49         5.69        11.08         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
        4.08        75.52        37.55         6.35        38.63        81.01 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT 
       18.08         1.84        46.82        21.01         3.88        13.22 
TCGA-X6-A7WB TCGA-X6-A7WD 
       18.08         8.52 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.72               0.07 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             74.66             143.41 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            12.555             18.920 
[1] "0.7 - 74.7 (12.6)"  "0.1 - 143.4 (18.9)"
[1] "hr=" "1.2"
D35V2, continuous
D35V3, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   13  9
  19Q GAIN WILD-TYPE 49 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     13    9
  19Q GAIN WILD-TYPE   49   43
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               13                 49
  MALE                  9                 43
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       1                         2    11
  19Q GAIN WILD-TYPE     3                         6    66
D35V4, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                2                  6
  WHITE                                   11                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   17 11
  20P GAIN WILD-TYPE 61 25
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                28                 86 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                11                 25 
$`20P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R 
       14.04         2.04        27.19        18.54        46.68        74.66 
TCGA-DX-A23Y TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A48P TCGA-DX-A6BB TCGA-FX-A3NJ 
        6.28        42.77        10.68        14.96        10.78         0.10 
TCGA-FX-A48G TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IF-A4AJ 
        0.07        12.62        41.33        80.48         3.22        25.22 
TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-N1-A6IA 
       31.76        13.58         5.92        11.70         2.37         4.08 
TCGA-PC-A5DL TCGA-SG-A6Z7 TCGA-UE-A6QU TCGA-X6-A7WC 
       37.55         3.88         0.72        27.16 

$`20P GAIN WILD-TYPE`
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       12.85        24.49        42.44        31.56        29.85         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       53.26        43.04         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 
       17.10        20.05        15.06        17.75         4.54        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U 
       19.30        24.26        12.26        27.22        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       25.08        11.47        54.87        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV 
        1.68        16.18         0.46         0.07        26.89         4.57 
TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI 
        4.14        23.97         0.10         9.80        21.37         8.94 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        1.38         7.13        37.12        28.21       143.41       116.88 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       73.28        22.62         6.28         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       36.39         5.26         0.49         5.69         4.47        11.08 
TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
        0.10        75.52         6.35        38.63        81.01        18.08 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT 
        1.84        46.82        18.08        18.18        21.01        13.22 
TCGA-X6-A7WB TCGA-X6-A7WD 
       18.08         8.52 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.07               0.07 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             80.48             143.41 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             13.10              18.13 
[1] "0.1 - 80.5 (13.1)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "1.8"
D36V2, continuous
D36V3, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   15 13
  20P GAIN WILD-TYPE 47 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     15   13
  20P GAIN WILD-TYPE   47   39
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               15                 47
  MALE                 13                 39
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       1                         1    19
  20P GAIN WILD-TYPE     3                         7    58
D36V4, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                1                  7
  WHITE                                   19                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   21 14
  20Q GAIN WILD-TYPE 57 22
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                35                 79 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                14                 22 
$`20Q GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        27.19        12.85        18.54        46.68 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LW TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A48P 
       74.66         6.28       108.13        42.77        10.68        14.96 
TCGA-DX-A6BB TCGA-FX-A3NJ TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-IE-A3OV 
       10.78         0.10         0.07         4.57        12.62        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 
        8.94         3.22        31.76       143.41        13.58         5.92 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-N1-A6IA TCGA-PC-A5DL TCGA-QQ-A5V9 
       11.70         5.26         2.37         4.08        37.55        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QU TCGA-X6-A7WC 
       18.08        21.01         3.88         0.72        27.16 

$`20Q GAIN WILD-TYPE`
TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       24.49        42.44        31.56        29.85         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87        27.81        60.30         8.58         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 
       43.04         9.04        23.08        70.49        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       15.06        17.75         4.54        14.99        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       28.80        34.88        64.18         9.73        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
       12.26        27.22        26.47        72.72        25.08        11.47 
TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       54.87        16.31         2.07         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 
        0.46         0.07        26.89         4.14        23.97         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       41.33         9.80        21.37         1.38         7.13        37.12 
TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE 
       25.22        28.21       116.88        73.28        22.62         6.28 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-MB-A5YA TCGA-MB-A8JL 
        1.05         3.91        71.70        36.39         0.49         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN 
        4.47        11.08         0.10        75.52         6.35        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VC TCGA-UE-A6QT TCGA-X6-A7WB 
       81.01        18.08         1.84        18.18        13.22        18.08 
TCGA-X6-A7WD 
        8.52 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.07               0.07 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            143.41             116.88 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             12.85              19.30 
[1] "0.1 - 143.4 (12.8)" "0.1 - 116.9 (19.3)"
[1] "hr=" "1.6"
D37V2, continuous
D37V3, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   18 17
  20Q GAIN WILD-TYPE 44 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     18   17
  20Q GAIN WILD-TYPE   44   35
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               18                 44
  MALE                 17                 35
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       1                         1    26
  20Q GAIN WILD-TYPE     3                         7    51
D37V4, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                1                  7
  WHITE                                   26                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED   15 11
  21Q GAIN WILD-TYPE 63 25
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                26                 88 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                11                 25 
$`21Q GAIN MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A2IZ TCGA-DX-A3LW TCGA-DX-A3U9 
        2.04        12.85        46.68         8.58       108.13        14.99 
TCGA-DX-A48K TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EJ 
       19.30         4.57         0.10        41.33        80.48         3.22 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-LI-A67I 
        7.13        25.22        13.58         5.92         1.05         5.26 
TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM TCGA-QQ-A5V9 TCGA-QQ-A5VC 
        4.47         4.08        37.55         6.35        46.82        18.18 
TCGA-UE-A6QT TCGA-UE-A6QU 
       13.22         0.72 

$`21Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04        27.19        24.49        18.54        42.44        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       29.85        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         9.70        53.26        43.04         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       23.08        70.49        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       34.88        64.18         9.73        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        26.47        72.72        25.08        11.47        54.87 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       10.78        16.31         2.07         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A43Z 
        0.46         0.10         0.07         0.07        26.89         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK 
       12.62        23.97         9.80        21.37         8.94         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 
       37.12        31.76        28.21       143.41       116.88        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W 
       22.62         6.28         3.91        71.70        36.39        11.70 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK 
        2.37         0.49         5.69        11.08         0.10        75.52 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VD 
       38.63        81.01        18.08         1.84        18.08        21.01 
TCGA-SG-A6Z7 TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        3.88        18.08        27.16         8.52 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.10               0.07 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            108.13             143.41 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            10.715             19.295 
[1] "0.1 - 108.1 (10.7)" "0.1 - 143.4 (19.3)"
[1] "hr=" "1.9"
D38V2, continuous
D38V3, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   13 13
  21Q GAIN WILD-TYPE 49 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     13   13
  21Q GAIN WILD-TYPE   49   39
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               13                 49
  MALE                 13                 39
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       2                         3    15
  21Q GAIN WILD-TYPE     2                         5    62
D38V4, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    2                  2
  BLACK OR AFRICAN AMERICAN                3                  5
  WHITE                                   15                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   17  9
  22Q GAIN WILD-TYPE 61 27
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                26                 88 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                 27 
$`22Q GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A3UA TCGA-DX-A48K TCGA-DX-A48O 
       14.04        27.19        12.85        10.68        19.30        27.22 
TCGA-DX-A48P TCGA-DX-A6BB TCGA-DX-A6BF TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 
       14.96        10.78         2.07        26.89         4.14        12.62 
TCGA-HS-A5N9 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AK TCGA-JV-A5VE TCGA-JV-A75J 
       41.33         8.94         3.22        31.76         6.28         3.91 
TCGA-MB-A5Y9 TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DP 
        2.37         4.47         4.08        37.55         6.35        18.08 
TCGA-QQ-A5V9 TCGA-QQ-A5VC 
       46.82        18.18 

$`22Q GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
        2.04        24.49        18.54        46.68        42.44        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       29.85        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        53.26        43.04 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB 
       15.06        17.75        42.77         4.54        14.99        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L 
       39.35        28.80        34.88        64.18         9.73        24.26 
TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       12.26        26.47        72.72        25.08        11.47        54.87 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ 
       16.31         7.36         1.68        16.18         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
        0.07         0.07         4.57        23.97         0.10         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
       80.48        21.37         1.38         7.13        37.12        25.22 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I 
       22.62         1.05        71.70        36.39        11.70         5.26 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DN 
        0.49         5.69        11.08         0.10        75.52        38.63 
TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT 
       81.01         1.84        18.08        21.01         3.88        13.22 
TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        0.72        18.08        27.16         8.52 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              2.07               0.07 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             46.82             143.41 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            12.735             19.295 
[1] "2.1 - 46.8 (12.7)"  "0.1 - 143.4 (19.3)"
[1] "hr=" "1.9"
D39V2, continuous
D39V3, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED   18  8
  22Q GAIN WILD-TYPE 44 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     18    8
  22Q GAIN WILD-TYPE   44   44
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               18                 44
  MALE                  8                 44
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       0                         4    19
  22Q GAIN WILD-TYPE     4                         4    58
D39V4, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                4                  4
  WHITE                                   19                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED    8  6
  XQ GAIN WILD-TYPE 70 30
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               14               100 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                30 
$`XQ GAIN MUTATED`
TCGA-DX-A1KZ TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A3LW TCGA-HB-A2OT TCGA-HS-A5N9 
       24.49         6.28        60.30       108.13        26.89        41.33 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IS-A3KA TCGA-JV-A75J TCGA-LI-A67I TCGA-QQ-A5VA 
       80.48         8.94        13.58         3.91         5.26        18.08 
TCGA-SG-A6Z7 TCGA-X6-A7WC 
        3.88        27.16 

$`XQ GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        27.19        12.85        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       42.44        31.56        29.85        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       66.87        27.81         8.58         9.70        53.26        43.04 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
        9.04        23.08        70.49        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       25.08        11.47        54.87        10.78        16.31         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
        7.36         1.68        16.18         0.46         0.10         0.07 
TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
        0.07         4.57         4.14        12.62        23.97         0.10 
TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
        9.80        21.37         3.22         1.38         7.13        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 
       25.22        31.76        28.21       143.41       116.88        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        22.62         6.28         1.05        71.70        36.39 
TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       11.70         2.37         0.49         5.69         4.47        11.08 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
        0.10         4.08        75.52        37.55         6.35        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD 
       81.01        18.08         1.84        46.82        18.18        21.01 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WD 
       13.22         0.72        18.08         8.52 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             3.88              0.07 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           108.13            143.41 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           21.285            17.425 
[1] "3.9 - 108.1 (21.3)" "0.1 - 143.4 (17.4)"
[1] "hr=" "1.1"
D40V2, continuous
D40V3, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    8  6
  XQ GAIN WILD-TYPE 54 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      8    6
  XQ GAIN WILD-TYPE   54   46
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               8                54
  MALE                 6                46
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       0                         1     9
  XQ GAIN WILD-TYPE     4                         7    68
D40V4, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               1                 7
  WHITE                                   9                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   14  2
  1P LOSS WILD-TYPE 64 34
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               16                98 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                34 
$`1P LOSS MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A3UA TCGA-DX-A3UF 
       27.19        24.49        18.54        46.68        10.68        64.18 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-FX-A3RE TCGA-FX-A48G TCGA-IS-A3K7 TCGA-IS-A3K8 
       11.47        54.87         0.07         0.07       143.41       116.88 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-MO-A47R TCGA-X6-A7WD 
       73.28        22.62         0.10         8.52 

$`1P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04         2.04        12.85        42.44        31.56        29.85 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       74.66         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        53.26        43.04         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75        42.77         4.54        14.99        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       28.80        34.88         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6BB 
       27.22        14.96        26.47        72.72        25.08        10.78 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS 
       16.31         2.07         7.36         1.68        16.18         0.46 
TCGA-FX-A3NJ TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.10        26.89         4.57         4.14        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
        0.10        41.33         9.80        80.48        21.37         8.94 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK 
        3.22         1.38         7.13        37.12        25.22        31.76 
TCGA-IS-A3K6 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       28.21        13.58         5.92         6.28         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA 
       71.70        36.39        11.70         5.26         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
        5.69         4.47        11.08         4.08        75.52        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 
        6.35        38.63        81.01        18.08         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU 
       18.08        18.18        21.01         3.88        13.22         0.72 
TCGA-X6-A7WB TCGA-X6-A7WC 
       18.08        27.16 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.07              0.10 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           143.41            108.13 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           23.555            16.705 
[1] "0.1 - 143.4 (23.6)" "0.1 - 108.1 (16.7)"
[1] "hr=" "4.1"
D41V2, continuous
D41V3, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   13  3
  1P LOSS WILD-TYPE 49 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     13    3
  1P LOSS WILD-TYPE   49   49
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              13                49
  MALE                 3                49
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       2                         1     9
  1P LOSS WILD-TYPE     2                         7    68
D41V4, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   2                 2
  BLACK OR AFRICAN AMERICAN               1                 7
  WHITE                                   9                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED   11  5
  1Q LOSS WILD-TYPE 67 31
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               16                98 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                5                31 
$`1Q LOSS MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A2J0 TCGA-DX-A6BA 
       27.19        24.49        18.54        46.68         9.70        54.87 
TCGA-DX-A6BF TCGA-FX-A2QS TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-IS-A3K7 
        2.07         0.46         0.07         4.57        12.62       143.41 
TCGA-IS-A3K8 TCGA-N1-A6IA TCGA-PC-A5DO TCGA-X6-A7WD 
      116.88         4.08        81.01         8.52 

$`1Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04         2.04        12.85        42.44        31.56        29.85 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       74.66         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
       60.30         8.58        53.26        43.04         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       42.77         4.54        14.99        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       28.80        34.88        64.18         9.73        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       11.47        10.78        16.31         7.36         1.68        16.18 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 
        0.10         0.07        26.89         4.14        23.97         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
       41.33         9.80        80.48        21.37         8.94         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        1.38         7.13        37.12        25.22        31.76        28.21 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
       13.58        73.28         5.92        22.62         6.28         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 
        3.91        71.70        36.39        11.70         5.26         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK 
        0.49         5.69         4.47        11.08         0.10        75.52 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       37.55         6.35        38.63        18.08         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU 
       18.08        18.18        21.01         3.88        13.22         0.72 
TCGA-X6-A7WB TCGA-X6-A7WC 
       18.08        27.16 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.07              0.07 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           143.41            108.13 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           15.580            17.915 
[1] "0.1 - 143.4 (15.6)" "0.1 - 108.1 (17.9)"
[1] "hr=" "1.5"
D42V2, continuous
D42V3, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED   11  5
  1Q LOSS WILD-TYPE 51 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     11    5
  1Q LOSS WILD-TYPE   51   47
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              11                51
  MALE                 5                47
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         1    10
  1Q LOSS WILD-TYPE     4                         7    67
D42V4, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               1                 7
  WHITE                                  10                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED   19 13
  2P LOSS WILD-TYPE 59 23
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               32                82 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               13                23 
$`2P LOSS MUTATED`
TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC 
       18.54        42.44         6.28        42.77        14.99        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48P TCGA-DX-A48R 
       28.80        34.88        64.18        24.26        14.96        26.47 
TCGA-DX-A48V TCGA-DX-A6BA TCGA-HB-A2OT TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       25.08        54.87        26.89        12.62        23.97         0.10 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
        9.80        80.48         3.22         7.13        37.12        25.22 
TCGA-IF-A4AK TCGA-JV-A5VE TCGA-K1-A3PN TCGA-MJ-A68H TCGA-PC-A5DO TCGA-PC-A5DP 
       31.76         6.28        71.70         4.47        81.01        18.08 
TCGA-QQ-A5V9 TCGA-X6-A7WB 
       46.82        18.08 

$`2P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       14.04         2.04        27.19        12.85        24.49        46.68 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        29.85        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        53.26        43.04 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A48J 
       15.06        17.75         4.54        10.68        44.45         9.73 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BB 
       19.30        12.26        27.22        72.72        11.47        10.78 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS 
       16.31         2.07         7.36         1.68        16.18         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N9 
        0.10         0.07         0.07         4.57         4.14        41.33 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       21.37         8.94         1.38        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        73.28         5.92        22.62         1.05         3.91 
TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       36.39        11.70         5.26         2.37         0.49         5.69 
TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
       11.08         0.10         4.08        75.52        37.55         6.35 
TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 
       38.63         1.84        18.08        18.18        21.01         3.88 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WC TCGA-X6-A7WD 
       13.22         0.72        27.16         8.52 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.10              0.07 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            81.01            143.41 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            25.15             13.81 
[1] "0.1 - 81.0 (25.1)"  "0.1 - 143.4 (13.8)"
[1] "hr=" "1.1"
D43V2, continuous
D43V3, binary
                   cls
clus                 0  1
  2P LOSS MUTATED   21 11
  2P LOSS WILD-TYPE 41 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     21   11
  2P LOSS WILD-TYPE   41   41
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              21                41
  MALE                11                41
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                         3    23
  2P LOSS WILD-TYPE     4                         5    54
D43V4, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               3                 5
  WHITE                                  23                54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED   14 13
  2Q LOSS WILD-TYPE 64 23
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               27                87 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               13                23 
$`2Q LOSS MUTATED`
TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD 
       18.54        42.44         6.28        42.77        14.99        28.80 
TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6BK TCGA-HB-A2OT TCGA-HB-A3YV 
       24.26        26.47        25.08        16.18        26.89         4.57 
TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ 
       12.62         0.10         9.80         3.22         7.13        37.12 
TCGA-IF-A4AK TCGA-JV-A5VE TCGA-JV-A5VF TCGA-MJ-A68H TCGA-PC-A5DM TCGA-PC-A5DP 
       31.76         6.28         1.05         4.47         6.35        18.08 
TCGA-SG-A6Z7 TCGA-X6-A7WB TCGA-X6-A7WC 
        3.88        18.08        27.16 

$`2Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       14.04         2.04        27.19        12.85        24.49        46.68 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        29.85        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        53.26        43.04 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       15.06        17.75         4.54        10.68        44.45        39.35 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       34.88        64.18         9.73        19.30        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       14.96        72.72        11.47        54.87        10.78        16.31 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
        2.07         7.36         1.68         0.46         0.10         0.07 
TCGA-FX-A48G TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EH 
        0.07         4.14        23.97        41.33        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        8.94         1.38        25.22        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A75J TCGA-K1-A3PN 
       13.58        73.28         5.92        22.62         3.91        71.70 
TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       36.39        11.70         5.26         2.37         0.49         5.69 
TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.08         0.10         4.08        75.52        37.55        38.63 
TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
       81.01         1.84        46.82        18.08        18.18        21.01 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WD 
       13.22         0.72         8.52 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.10              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            42.77            143.41 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            16.18             18.08 
[1] "0.1 - 42.8 (16.2)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "2.9"
D44V2, continuous
D44V3, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED   16 11
  2Q LOSS WILD-TYPE 46 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     16   11
  2Q LOSS WILD-TYPE   46   41
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              16                46
  MALE                11                41
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         4    18
  2Q LOSS WILD-TYPE     4                         4    59
D44V4, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               4                 4
  WHITE                                  18                59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED   11  9
  3P LOSS WILD-TYPE 67 27
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               20                94 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                27 
$`3P LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LS 
        2.04        27.19        18.54        74.66         6.28         9.04 
TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A48N TCGA-DX-A48R 
       23.08        17.10        20.05        10.68        12.26        26.47 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-JV-A5VF 
        4.57         4.14         3.22         7.13        37.12         1.05 
TCGA-PC-A5DL TCGA-PC-A5DM 
       37.55         6.35 

$`3P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04        12.85        24.49        46.68        42.44        31.56 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       29.85         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW 
        8.58         9.70        53.26        43.04        70.49       108.13 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB 
       15.06        17.75        42.77         4.54        14.99        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
       24.26        27.22        14.96        72.72        25.08        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       54.87        10.78        16.31         2.07         7.36         1.68 
TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
       16.18         0.46         0.10         0.07         0.07        26.89 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       12.62        23.97         0.10        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
       21.37         8.94         1.38        25.22        31.76        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
      143.41       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I 
        6.28         3.91        71.70        36.39        11.70         5.26 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
        2.37         0.49         5.69         4.47        11.08         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 
        4.08        75.52        38.63        81.01        18.08         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT 
       46.82        18.08        18.18        21.01         3.88        13.22 
TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        0.72        18.08        27.16         8.52 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             1.05              0.07 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            74.66            143.41 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            11.47             18.08 
[1] "1.1 - 74.7 (11.5)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "2.5"
D45V2, continuous
D45V3, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    9 11
  3P LOSS WILD-TYPE 53 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      9   11
  3P LOSS WILD-TYPE   53   41
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               9                53
  MALE                11                41
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       0                         1    14
  3P LOSS WILD-TYPE     4                         7    63
D45V4, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               1                 7
  WHITE                                  14                63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED   14 10
  3Q LOSS WILD-TYPE 64 26
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               24                90 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10                26 
$`3Q LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y 
        2.04        27.19        18.54        46.68        74.66         6.28 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A48N 
        9.04        23.08        17.10        20.05        10.68        12.26 
TCGA-DX-A48R TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A6BZ 
       26.47         4.57         4.14        80.48         3.22         7.13 
TCGA-IF-A3RQ TCGA-JV-A5VF TCGA-MJ-A68H TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DM 
       37.12         1.05         4.47         0.10        37.55         6.35 

$`3Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04        12.85        24.49        42.44        31.56        29.85 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 
        9.70        53.26        43.04        70.49       108.13        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75        42.77         4.54        14.99        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       28.80        34.88        64.18         9.73        19.30        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       27.22        14.96        72.72        25.08        11.47        54.87 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       10.78        16.31         2.07         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A5W3 
        0.46         0.10         0.07         0.07        26.89        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI 
       23.97         0.10        41.33         9.80        21.37         8.94 
TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        1.38        25.22        31.76        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J 
       13.58        73.28         5.92        22.62         6.28         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA 
       71.70        36.39        11.70         5.26         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO 
        5.69        11.08         4.08        75.52        38.63        81.01 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
       18.08         1.84        46.82        18.08        18.18        21.01 
TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        3.88        13.22         0.72        18.08        27.16         8.52 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.10              0.07 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            80.48            143.41 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            11.47             18.08 
[1] "0.1 - 80.5 (11.5)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "1.9"
D46V2, continuous
D46V3, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   11 13
  3Q LOSS WILD-TYPE 51 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     11   13
  3Q LOSS WILD-TYPE   51   39
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              11                51
  MALE                13                39
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         2    15
  3Q LOSS WILD-TYPE     3                         6    62
D46V4, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               2                 6
  WHITE                                  15                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   10  8
  4P LOSS WILD-TYPE 68 28
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               18                96 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                8                28 
$`4P LOSS MUTATED`
TCGA-DX-A2IZ TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A3UE 
        8.58        23.08        42.77        10.68        28.80        34.88 
TCGA-DX-A48L TCGA-DX-A48R TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EK TCGA-IW-A3M5 
       24.26        26.47         4.14        12.62         1.38         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-LI-A67I TCGA-MO-A47R TCGA-PC-A5DM TCGA-QQ-A5V9 
       22.62         1.05         5.26         0.10         6.35        46.82 

$`4P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        42.44        31.56        29.85        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 
       76.41        66.87         6.28        27.81        60.30         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       53.26        43.04         9.04        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB 
       20.05        15.06        17.75         4.54        14.99        44.45 
TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       39.35        64.18         9.73        19.30        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       14.96        72.72        25.08        11.47        54.87        10.78 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS 
       16.31         2.07         7.36         1.68        16.18         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 
        0.10         0.07         0.07        26.89         4.57        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
        0.10        41.33         9.80        80.48        21.37         8.94 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        3.22         7.13        37.12        25.22        31.76        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J 
      143.41       116.88        13.58        73.28         6.28         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       71.70        36.39        11.70         2.37         0.49         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
        4.47        11.08         4.08        75.52        37.55        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
       81.01        18.08         1.84        18.08        18.18        21.01 
TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        3.88        13.22         0.72        18.08        27.16         8.52 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.10              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            46.82            143.41 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            11.65             18.08 
[1] "0.1 - 46.8 (11.6)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "2.3"
D47V2, continuous
D47V3, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   10  8
  4P LOSS WILD-TYPE 52 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     10    8
  4P LOSS WILD-TYPE   52   44
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              10                52
  MALE                 8                44
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       2                         1    14
  4P LOSS WILD-TYPE     2                         7    63
D47V4, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   2                 2
  BLACK OR AFRICAN AMERICAN               1                 7
  WHITE                                  14                63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   16  6
  4Q LOSS WILD-TYPE 62 30
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               22                92 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                6                30 
$`4Q LOSS MUTATED`
TCGA-DX-A23R TCGA-DX-A2IZ TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UD 
       74.66         8.58        23.08        42.77        10.68        28.80 
TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A6BA TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-IE-A4EH 
       24.26        26.47        54.87         4.14         0.10        21.37 
TCGA-IE-A4EK TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-KF-A41W TCGA-LI-A67I 
        1.38         5.92        22.62         1.05        11.70         5.26 
TCGA-MO-A47R TCGA-PC-A5DM TCGA-QQ-A5V9 TCGA-X6-A7WD 
        0.10         6.35        46.82         8.52 

$`4Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       46.68        42.44        31.56        29.85         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87         6.28        27.81        60.30         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       43.04         9.04        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       15.06        17.75         4.54        14.99        44.45        39.35 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       34.88        64.18         9.73        19.30        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       14.96        72.72        25.08        11.47        10.78        16.31 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ 
        2.07         7.36         1.68        16.18         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07         0.07        26.89         4.57        12.62        23.97 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ 
       41.33         9.80        80.48         8.94         3.22         7.13 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       37.12        25.22        31.76        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       13.58        73.28         6.28         3.91        71.70        36.39 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-N1-A6IA 
        2.37         0.49         5.69         4.47        11.08         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 
       75.52        37.55        38.63        81.01        18.08         1.84 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU 
       18.08        18.18        21.01         3.88        13.22         0.72 
TCGA-X6-A7WB TCGA-X6-A7WC 
       18.08        27.16 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.10              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            74.66            143.41 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            11.19             18.08 
[1] "0.1 - 74.7 (11.2)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "1.2"
D48V2, continuous
D48V3, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   14  8
  4Q LOSS WILD-TYPE 48 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     14    8
  4Q LOSS WILD-TYPE   48   44
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              14                48
  MALE                 8                44
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       2                         1    16
  4Q LOSS WILD-TYPE     2                         7    61
D48V4, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   2                 2
  BLACK OR AFRICAN AMERICAN               1                 7
  WHITE                                  16                61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    8  1
  5P LOSS WILD-TYPE 70 35
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9               105 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                35 
$`5P LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A3UA 
        2.04        24.49        74.66        23.08        20.05        10.68 
TCGA-IS-A3K7 TCGA-KF-A41W TCGA-MB-A8JL 
      143.41        11.70         5.69 

$`5P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04        27.19        12.85        18.54        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       31.56        29.85         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        53.26        43.04 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 
        9.04        70.49       108.13        17.10        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        14.99        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
       27.22        14.96        26.47        72.72        25.08        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       54.87        10.78        16.31         2.07         7.36         1.68 
TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
       16.18         0.46         0.10         0.07         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
        4.57         4.14        12.62        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37         8.94         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
        7.13        37.12        25.22        31.76        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
       13.58        73.28         5.92        22.62         6.28         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA 
        3.91        71.70        36.39         5.26         2.37         0.49 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
        4.47        11.08         0.10         4.08        75.52        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 
        6.35        38.63        81.01        18.08         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU 
       18.08        18.18        21.01         3.88        13.22         0.72 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       18.08        27.16         8.52 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             2.04              0.07 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           143.41            116.88 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            20.05             17.75 
[1] "2.0 - 143.4 (20.1)" "0.1 - 116.9 (17.8)"
[1] "hr=" "3.6"
D49V2, continuous
D49V3, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    5  4
  5P LOSS WILD-TYPE 57 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5    4
  5P LOSS WILD-TYPE   57   48
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               5                57
  MALE                 4                48
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       0                         0     6
  5P LOSS WILD-TYPE     4                         8    71
D49V4, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               0                 8
  WHITE                                   6                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED   13  2
  5Q LOSS WILD-TYPE 65 34
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               15                99 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                34 
$`5Q LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A3UA 
        2.04        24.49        74.66        23.08        20.05        10.68 
TCGA-FX-A2QS TCGA-HB-A2OT TCGA-IE-A4EH TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-KF-A41W 
        0.46        26.89        21.37         7.13        25.22        11.70 
TCGA-MB-A8JL TCGA-X6-A7WC TCGA-X6-A7WD 
        5.69        27.16         8.52 

$`5Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04        27.19        12.85        18.54        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       31.56        29.85         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        53.26        43.04 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 
        9.04        70.49       108.13        17.10        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        14.99        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
       27.22        14.96        26.47        72.72        25.08        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       54.87        10.78        16.31         2.07         7.36         1.68 
TCGA-DX-A6BK TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A43Z 
       16.18         0.10         0.07         0.07         4.57         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       12.62        23.97         0.10        41.33         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 
        8.94         3.22         1.38        37.12        31.76        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
      143.41       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I 
        6.28         1.05         3.91        71.70        36.39         5.26 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA 
        2.37         0.49         4.47        11.08         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
       75.52        37.55         6.35        38.63        81.01        18.08 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 
        1.84        46.82        18.08        18.18        21.01         3.88 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB 
       13.22         0.72        18.08 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.46              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            74.66            143.41 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            20.05             17.75 
[1] "0.5 - 74.7 (20.1)"  "0.1 - 143.4 (17.8)"
[1] "hr=" "1.9"
D50V2, continuous
D50V3, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    9  6
  5Q LOSS WILD-TYPE 53 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      9    6
  5Q LOSS WILD-TYPE   53   46
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               9                53
  MALE                 6                46
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       0                         1    11
  5Q LOSS WILD-TYPE     4                         7    66
D50V4, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               1                 7
  WHITE                                  11                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   22  6
  6P LOSS WILD-TYPE 56 30
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               28                86 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                30 
$`6P LOSS MUTATED`
TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3UA 
       24.49        74.66        23.08        17.10        20.05        10.68 
TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       39.35        64.18        19.30        24.26        27.22        14.96 
TCGA-DX-A48V TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6BK TCGA-FX-A48G 
       25.08        54.87        10.78         2.07        16.18         0.07 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A3OV TCGA-IW-A3M6 TCGA-K1-A3PN TCGA-K1-A3PO 
        4.14        12.62        80.48        22.62        71.70        36.39 
TCGA-MB-A8JL TCGA-PC-A5DL TCGA-QQ-A5VD TCGA-X6-A7WC 
        5.69        37.55        21.01        27.16 

$`6P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        27.19        12.85        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       42.44        31.56        29.85         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 
       43.04         9.04        70.49       108.13        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE 
       42.77         4.54        14.99        44.45        28.80        34.88 
TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BE 
        9.73        12.26        26.47        72.72        11.47        16.31 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A2OT 
        7.36         1.68         0.46         0.10         0.07        26.89 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH 
        4.57        23.97         0.10        41.33         9.80        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
        8.94         3.22         1.38         7.13        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       31.76        28.21       143.41       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-KF-A41W TCGA-LI-A67I 
        5.92         6.28         1.05         3.91        11.70         5.26 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA 
        2.37         0.49         4.47        11.08         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 
       75.52         6.35        38.63        81.01        18.08         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU 
       46.82        18.08        18.18         3.88        13.22         0.72 
TCGA-X6-A7WB TCGA-X6-A7WD 
       18.08         8.52 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.07              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            80.48            143.41 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           22.850            14.515 
[1] "0.1 - 80.5 (22.9)"  "0.1 - 143.4 (14.5)"
[1] "hr=" "1.9"
D51V2, continuous
D51V3, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   16 12
  6P LOSS WILD-TYPE 46 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     16   12
  6P LOSS WILD-TYPE   46   40
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              16                46
  MALE                12                40
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       1                         0    25
  6P LOSS WILD-TYPE     3                         8    52
D51V4, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               0                 8
  WHITE                                  25                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   12  5
  6Q LOSS WILD-TYPE 66 31
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               17                97 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                5                31 
$`6Q LOSS MUTATED`
TCGA-DX-A23R TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48P 
       74.66        42.77        10.68        64.18        24.26        14.96 
TCGA-DX-A48V TCGA-DX-A6BA TCGA-FX-A48G TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-IE-A3OV 
       25.08        54.87         0.07         4.14         0.10        80.48 
TCGA-MB-A8JL TCGA-PC-A5DO TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-X6-A7WC 
        5.69        81.01        21.01         3.88        27.16 

$`6Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       46.68        42.44        31.56        29.85         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       53.26        43.04         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 
       17.10        20.05        15.06        17.75         4.54        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       44.45        39.35        28.80        34.88         9.73        19.30 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BB 
       12.26        27.22        26.47        72.72        11.47        10.78 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS 
       16.31         2.07         7.36         1.68        16.18         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.10         0.07        26.89         4.57        12.62        23.97 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
       41.33         9.80        21.37         8.94         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        7.13        37.12        25.22        31.76        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62         6.28 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I 
        1.05         3.91        71.70        36.39        11.70         5.26 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA 
        2.37         0.49         4.47        11.08         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 
       75.52        37.55         6.35        38.63        18.08         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB 
       46.82        18.08        18.18        13.22         0.72        18.08 
TCGA-X6-A7WD 
        8.52 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.07              0.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            81.01            143.41 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            24.26             17.10 
[1] "0.1 - 81.0 (24.3)"  "0.1 - 143.4 (17.1)"
[1] "hr=" "1.4"
D52V2, continuous
D52V3, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   12  5
  6Q LOSS WILD-TYPE 50 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     12    5
  6Q LOSS WILD-TYPE   50   47
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              12                50
  MALE                 5                47
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       0                         0    15
  6Q LOSS WILD-TYPE     4                         8    62
D52V4, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               0                 8
  WHITE                                  15                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED   12  4
  7P LOSS WILD-TYPE 66 32
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               16                98 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4                32 
$`7P LOSS MUTATED`
TCGA-DX-A23Y TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A3UD TCGA-DX-A48P TCGA-DX-A48U 
        6.28        17.10        42.77        28.80        14.96        72.72 
TCGA-DX-A48V TCGA-DX-A6BF TCGA-DX-A6BH TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IW-A3M6 
       25.08         2.07         1.68        23.97        80.48        22.62 
TCGA-KF-A41W TCGA-MB-A5YA TCGA-PC-A5DM TCGA-PC-A5DO 
       11.70         0.49         6.35        81.01 

$`7P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        42.44        31.56        29.85        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       53.26        43.04         9.04        23.08        70.49       108.13 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       20.05        15.06        17.75         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       44.45        39.35        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A6B9 TCGA-DX-A6BA 
       24.26        12.26        27.22        26.47        11.47        54.87 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ 
       10.78        16.31         7.36        16.18         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        0.07         0.07        26.89         4.57         4.14        12.62 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
        0.10        41.33         9.80        21.37         8.94         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        1.38         7.13        37.12        25.22        31.76        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE 
      143.41       116.88        13.58        73.28         5.92         6.28 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 
        1.05         3.91        71.70        36.39         5.26         2.37 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
        5.69         4.47        11.08         0.10         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       37.55        38.63        18.08         1.84        46.82        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB 
       18.18        21.01         3.88        13.22         0.72        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD 
       27.16         8.52 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.49              0.07 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            81.01            143.41 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           19.860            17.915 
[1] "0.5 - 81.0 (19.9)"  "0.1 - 143.4 (17.9)"
[1] "hr=" "1.6"
D53V2, continuous
D53V3, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    6 10
  7P LOSS WILD-TYPE 56 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      6   10
  7P LOSS WILD-TYPE   56   42
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               6                56
  MALE                10                42
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       1                         0    13
  7P LOSS WILD-TYPE     3                         8    64
D53V4, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               0                 8
  WHITE                                  13                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED    7  7
  7Q LOSS WILD-TYPE 71 29
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               14               100 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                7                29 
$`7Q LOSS MUTATED`
TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48P TCGA-DX-A6BF 
       17.10        42.77        28.80         9.73        14.96         2.07 
TCGA-DX-A6BH TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IW-A3M5 TCGA-MB-A5YA TCGA-PC-A5DM 
        1.68        37.12        25.22         5.92         0.49         6.35 
TCGA-PC-A5DP TCGA-QQ-A5VA 
       18.08        18.08 

$`7Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        42.44        31.56        29.85        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        53.26        43.04         9.04        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 
      108.13        20.05        15.06        17.75         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K 
       10.68        44.45        39.35        34.88        64.18        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       24.26        12.26        27.22        26.47        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BK 
       11.47        54.87        10.78        16.31         7.36        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV 
        0.46         0.10         0.07         0.07        26.89         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.14        12.62        23.97         0.10        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
       80.48        21.37         8.94         3.22         1.38         7.13 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       31.76        28.21       143.41       116.88        13.58        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       22.62         6.28         1.05         3.91        71.70        36.39 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       11.70         5.26         2.37         5.69         4.47        11.08 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
        0.10         4.08        75.52        37.55        38.63        81.01 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT 
        1.84        46.82        18.18        21.01         3.88        13.22 
TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        0.72        18.08        27.16         8.52 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.49              0.07 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            42.77            143.41 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            16.03             18.13 
[1] "0.5 - 42.8 (16.0)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "2.6"
D54V2, continuous
D54V3, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    6  8
  7Q LOSS WILD-TYPE 56 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      6    8
  7Q LOSS WILD-TYPE   56   44
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               6                56
  MALE                 8                44
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       0                         1    13
  7Q LOSS WILD-TYPE     4                         7    64
D54V4, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               1                 7
  WHITE                                  13                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   18  6
  8P LOSS WILD-TYPE 60 30
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               24                90 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                6                30 
$`8P LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3LS 
        2.04        27.19        24.49        42.44         6.28         9.04 
TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48R 
       42.77        10.68        44.45         9.73        19.30        26.47 
TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3RE TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5N9 
       16.18         0.46         0.07         4.14         0.10        41.33 
TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-JV-A5VE TCGA-KF-A41W TCGA-MB-A8JL TCGA-SG-A6Z7 
        7.13       143.41         6.28        11.70         5.69         3.88 

$`8P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04        12.85        18.54        46.68        31.56        29.85 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU 
        8.58         9.70        53.26        43.04        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 
      108.13        17.10        20.05        15.06        17.75         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L 
       14.99        39.35        28.80        34.88        64.18        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
       12.26        27.22        14.96        72.72        25.08        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       54.87        10.78        16.31         2.07         7.36         1.68 
TCGA-FX-A3NJ TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.10         0.07        26.89         4.57        12.62        23.97 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37         8.94         3.22         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA 
       37.12        25.22        31.76        28.21       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       73.28         5.92        22.62         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J 
       36.39         5.26         2.37         0.49         4.47        11.08 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
        0.10         4.08        75.52        37.55         6.35        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       81.01        18.08         1.84        46.82        18.08        18.18 
TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       21.01        13.22         0.72        18.08        27.16         8.52 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.07              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           143.41            116.88 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           10.205            18.130 
[1] "0.1 - 143.4 (10.2)" "0.1 - 116.9 (18.1)"
[1] "hr=" "1"  
D55V2, continuous
D55V3, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   15  9
  8P LOSS WILD-TYPE 47 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     15    9
  8P LOSS WILD-TYPE   47   43
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              15                47
  MALE                 9                43
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       0                         2    15
  8P LOSS WILD-TYPE     4                         6    62
D55V4, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               2                 6
  WHITE                                  15                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    9  5
  8Q LOSS WILD-TYPE 69 31
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               14               100 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5                31 
$`8Q LOSS MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A48J 
       27.19        24.49        42.44         6.28         9.04         9.73 
TCGA-DX-A48L TCGA-HB-A43Z TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-JV-A5VE 
       24.26         4.14         3.22         7.13       143.41         6.28 
TCGA-KF-A41W TCGA-PC-A5DO 
       11.70        81.01 

$`8Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 
       14.04         2.04        12.85        18.54        46.68        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       29.85        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT 
       60.30         8.58         9.70        53.26        43.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       42.77         4.54        14.99        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       28.80        34.88        64.18        19.30        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        26.47        72.72        25.08        11.47        54.87 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       10.78        16.31         2.07         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV 
        0.46         0.10         0.07         0.07        26.89         4.57 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       12.62        23.97         0.10        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK 
       21.37         8.94         1.38        37.12        25.22        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
       28.21       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 
        1.05         3.91        71.70        36.39         5.26         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA 
        0.49         5.69         4.47        11.08         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 
       75.52        37.55         6.35        38.63        18.08         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT 
       46.82        18.08        18.18        21.01         3.88        13.22 
TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        0.72        18.08        27.16         8.52 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             3.22              0.07 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           143.41            116.88 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           10.715            18.080 
[1] "3.2 - 143.4 (10.7)" "0.1 - 116.9 (18.1)"
[1] "hr=" "1"  
D56V2, continuous
D56V3, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED   10  4
  8Q LOSS WILD-TYPE 52 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     10    4
  8Q LOSS WILD-TYPE   52   48
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              10                52
  MALE                 4                48
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       0                         2     8
  8Q LOSS WILD-TYPE     4                         6    69
D56V4, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               2                 6
  WHITE                                   8                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   23 11
  9P LOSS WILD-TYPE 55 25
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               34                80 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               11                25 
$`9P LOSS MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3LW 
       14.04        12.85        66.87         6.28         9.04       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U7 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J 
       17.10        20.05        42.77        28.80        64.18         9.73 
TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6BA TCGA-DX-A6BF TCGA-FX-A2QS TCGA-FX-A3RE 
       26.47        25.08        54.87         2.07         0.46         0.07 
TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IS-A3K7 
       26.89         0.10        80.48         8.94         3.22       143.41 
TCGA-IW-A3M5 TCGA-JV-A75J TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MO-A47R TCGA-N1-A6IA 
        5.92         3.91         2.37         5.69         0.10         4.08 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5VC TCGA-UE-A6QU 
       38.63        81.01        18.18         0.72 

$`9P LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        27.19        24.49        18.54        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23Z 
       31.56        29.85        74.66         5.26        76.41        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT 
       60.30         8.58         9.70        53.26        43.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       70.49        15.06        17.75         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       44.45        39.35        34.88        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       27.22        14.96        72.72        11.47        10.78        16.31 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A3NJ TCGA-FX-A48G TCGA-HB-A3YV 
        7.36         1.68        16.18         0.10         0.07         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH 
        4.14        12.62        23.97        41.33         9.80        21.37 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        1.38         7.13        37.12        25.22        31.76        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
      116.88        13.58        73.28        22.62         6.28         1.05 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5YA TCGA-MJ-A68H 
       71.70        36.39        11.70         5.26         0.49         4.47 
TCGA-MJ-A68J TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A5V2 
       11.08        75.52        37.55         6.35        18.08         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WB 
       46.82        18.08        21.01         3.88        13.22        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD 
       27.16         8.52 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.07              0.07 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           143.41            116.88 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           13.445            18.080 
[1] "0.1 - 143.4 (13.4)" "0.1 - 116.9 (18.1)"
[1] "hr=" "1.1"
D57V2, continuous
D57V3, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   21 13
  9P LOSS WILD-TYPE 41 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     21   13
  9P LOSS WILD-TYPE   41   39
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              21                41
  MALE                13                39
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       2                         3    25
  9P LOSS WILD-TYPE     2                         5    52
D57V4, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   2                 2
  BLACK OR AFRICAN AMERICAN               3                 5
  WHITE                                  25                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   12 11
  9Q LOSS WILD-TYPE 66 25
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               23                91 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11                25 
$`9Q LOSS MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3UD 
       14.04        12.85         6.28         9.04       108.13        28.80 
TCGA-DX-A48J TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6BF TCGA-HB-A2OT TCGA-HS-A5N8 
        9.73        26.47        25.08         2.07        26.89         0.10 
TCGA-IE-A3OV TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A75J TCGA-MB-A8JL 
       80.48       143.41        13.58         5.92         3.91         5.69 
TCGA-MJ-A68H TCGA-MO-A47R TCGA-PC-A5DO TCGA-SG-A6Z7 TCGA-UE-A6QU 
        4.47         0.10        81.01         3.88         0.72 

$`9Q LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        27.19        24.49        18.54        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        29.85        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        53.26        43.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       23.08        70.49        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       42.77         4.54        14.99        10.68        44.45        39.35 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       34.88        64.18        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       14.96        72.72        11.47        54.87        10.78        16.31 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
        7.36         1.68        16.18         0.46         0.10         0.07 
TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 
        0.07         4.57         4.14        12.62        23.97        41.33 
TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
        9.80        21.37         8.94         3.22         1.38         7.13 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M4 
       37.12        25.22        31.76        28.21       116.88        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W 
       22.62         6.28         1.05        71.70        36.39        11.70 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68J TCGA-N1-A6IA TCGA-PC-A5DK 
        5.26         2.37         0.49        11.08         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       37.55         6.35        38.63        18.08         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WC 
       18.08        18.18        21.01        13.22        18.08        27.16 
TCGA-X6-A7WD 
        8.52 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.10              0.07 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           143.41            116.88 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             9.73             18.18 
[1] "0.1 - 143.4 (9.7)"  "0.1 - 116.9 (18.2)"
[1] "hr=" "1.8"
D58V2, continuous
D58V3, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   14  9
  9Q LOSS WILD-TYPE 48 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     14    9
  9Q LOSS WILD-TYPE   48   43
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              14                48
  MALE                 9                43
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       2                         3    15
  9Q LOSS WILD-TYPE     2                         5    62
D58V4, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   2                 2
  BLACK OR AFRICAN AMERICAN               3                 5
  WHITE                                  15                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   36 16
  10P LOSS WILD-TYPE 42 20
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                52                 62 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                16                 20 
$`10P LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3U9 
        2.04        27.19        18.54        74.66         6.28        14.99 
TCGA-DX-A3UA TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48P TCGA-DX-A48R 
       10.68        34.88        64.18        19.30        14.96        26.47 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6BK TCGA-FX-A2QS 
       11.47        54.87        10.78         2.07        16.18         0.46 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        0.07         0.07        26.89         4.57         4.14        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AJ 
       23.97         0.10        80.48         8.94         3.22        25.22 
TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J 
       31.76       143.41         5.92        22.62         6.28         3.91 
TCGA-K1-A3PN TCGA-KF-A41W TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MO-A47R 
       71.70        11.70         0.49         5.69         4.47         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V9 
        4.08        75.52        37.55        81.01        18.08        46.82 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QU TCGA-X6-A7WD 
       18.18        21.01         0.72         8.52 

$`10P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04        12.85        24.49        46.68        42.44        31.56 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       29.85         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        53.26        43.04         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A48J 
       42.77         4.54        44.45        39.35        28.80         9.73 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6BE 
       24.26        12.26        27.22        72.72        25.08        16.31 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A3NJ TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH 
        7.36         1.68         0.10        41.33         9.80        21.37 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA 
        1.38         7.13        37.12        28.21       116.88        13.58 
TCGA-IW-A3M4 TCGA-JV-A5VF TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MJ-A68J 
       73.28         1.05        36.39         5.26         2.37        11.08 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-SG-A6Z7 TCGA-UE-A6QT 
        6.35        38.63         1.84        18.08         3.88        13.22 
TCGA-X6-A7WB TCGA-X6-A7WC 
       18.08        27.16 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.07               0.10 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            143.41             116.88 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             13.79              20.71 
[1] "0.1 - 143.4 (13.8)" "0.1 - 116.9 (20.7)"
[1] "hr=" "1.2"
D59V2, continuous
D59V3, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   37 15
  10P LOSS WILD-TYPE 25 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     37   15
  10P LOSS WILD-TYPE   25   37
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               37                 25
  MALE                 15                 37
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       3                         5    37
  10P LOSS WILD-TYPE     1                         3    40
D59V4, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    3                  1
  BLACK OR AFRICAN AMERICAN                5                  3
  WHITE                                   37                 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"

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   41 21
  10Q LOSS WILD-TYPE 37 15
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                62                 52 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                21                 15 
$`10Q LOSS MUTATED`
TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23Y TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA 
       27.19        18.54         6.28        42.77        14.99        10.68 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O 
       39.35        34.88        64.18        19.30        24.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       14.96        26.47        72.72        11.47        54.87        10.78 
TCGA-DX-A6BF TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
        2.07        16.18         0.46         0.10         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       26.89         4.57         4.14        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
       41.33        80.48        21.37         8.94         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3KA 
        7.13        25.22        31.76        28.21       143.41        13.58 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-KF-A41W 
       22.62         6.28         1.05         3.91        71.70        11.70 
TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM 
        0.49         4.47         0.10         4.08        37.55         6.35 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QU 
       81.01        18.08        46.82        18.18        21.01         0.72 
TCGA-X6-A7WB TCGA-X6-A7WD 
       18.08         8.52 

$`10Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04         2.04        12.85        24.49        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        29.85        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        53.26        43.04 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A48J 
       15.06        17.75         4.54        44.45        28.80         9.73 
TCGA-DX-A48N TCGA-DX-A48V TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-HS-A5NA 
       12.26        25.08        16.31         7.36         1.68         9.80 
TCGA-IF-A3RQ TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-K1-A3PO TCGA-LI-A67I 
       37.12       116.88        73.28         5.92        36.39         5.26 
TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MJ-A68J TCGA-PC-A5DK TCGA-PC-A5DN TCGA-QQ-A5V2 
        2.37         5.69        11.08        75.52        38.63         1.84 
TCGA-QQ-A5VA TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WC 
       18.08         3.88        13.22        27.16 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.07               1.68 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            143.41             116.88 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            15.585             19.065 
[1] "0.1 - 143.4 (15.6)" "1.7 - 116.9 (19.1)"
[1] "hr=" "1.5"
D60V2, continuous
D60V3, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   44 18
  10Q LOSS WILD-TYPE 18 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     44   18
  10Q LOSS WILD-TYPE   18   34
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               44                 18
  MALE                 18                 34
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       3                         6    47
  10Q LOSS WILD-TYPE     1                         2    30
D60V4, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    3                  1
  BLACK OR AFRICAN AMERICAN                6                  2
  WHITE                                   47                 30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   28 16
  11P LOSS WILD-TYPE 50 20
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                44                 70 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                16                 20 
$`11P LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R 
        2.04        27.19        24.49        18.54        42.44        74.66 
TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3LY 
        6.28         9.70        53.26        23.08       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48N 
       20.05        14.99        28.80        64.18        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A6BF TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV 
       27.22        14.96         2.07         0.07        26.89         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A6BZ 
        4.14        12.62        23.97         0.10        41.33         7.13 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF 
       37.12        25.22        31.76         5.92        22.62         1.05 
TCGA-K1-A3PN TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DO TCGA-SG-A6Z7 
       71.70         0.10        37.55         6.35        81.01         3.88 
TCGA-X6-A7WB TCGA-X6-A7WC 
       18.08        27.16 

$`11P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       14.04        12.85        46.68        31.56        29.85         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J4 
       76.41        66.87        27.81        60.30         8.58        43.04 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
        9.04        70.49        15.06        17.75        42.77         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       10.68        44.45        39.35        34.88         9.73        19.30 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       26.47        72.72        25.08        11.47        54.87        10.78 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ 
       16.31         7.36         1.68        16.18         0.46         0.10 
TCGA-FX-A48G TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
        0.07         9.80        80.48        21.37         8.94         3.22 
TCGA-IE-A4EK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
        1.38        28.21       143.41       116.88        13.58        73.28 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 
        6.28         3.91        36.39        11.70         5.26         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-N1-A6IA TCGA-PC-A5DK 
        0.49         5.69         4.47        11.08         4.08        75.52 
TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       38.63        18.08         1.84        46.82        18.08        18.18 
TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WD 
       21.01        13.22         0.72         8.52 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.07               0.07 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            108.13             143.41 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            21.335             15.620 
[1] "0.1 - 108.1 (21.3)" "0.1 - 143.4 (15.6)"
[1] "hr=" "1.2"
D61V2, continuous
D61V3, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   25 19
  11P LOSS WILD-TYPE 37 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     25   19
  11P LOSS WILD-TYPE   37   33
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               25                 37
  MALE                 19                 33
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       2                         2    28
  11P LOSS WILD-TYPE     2                         6    49
D61V4, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    2                  2
  BLACK OR AFRICAN AMERICAN                2                  6
  WHITE                                   28                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   23 13
  11Q LOSS WILD-TYPE 55 23
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                36                 78 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                13                 23 
$`11Q LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R 
        2.04        27.19        24.49        18.54        42.44        74.66 
TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A3U9 
        6.28         9.70        53.26        23.08        20.05        14.99 
TCGA-DX-A3UD TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6BA 
       28.80        24.26        12.26        26.47        72.72        54.87 
TCGA-DX-A6BF TCGA-DX-A6BK TCGA-FX-A2QS TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 
        2.07        16.18         0.46        26.89         4.57        12.62 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK 
        0.10        41.33        80.48         7.13        37.12        31.76 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-LI-A67I TCGA-SG-A6Z7 TCGA-X6-A7WC 
        5.92        22.62         1.05         5.26         3.88        27.16 

$`11Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       14.04        12.85        46.68        31.56        29.85         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J4 
       76.41        66.87        27.81        60.30         8.58        43.04 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 
        9.04        70.49       108.13        17.10        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE 
       42.77         4.54        10.68        44.45        39.35        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48V 
       64.18         9.73        19.30        27.22        14.96        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A3NJ 
       11.47        10.78        16.31         7.36         1.68         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EH 
        0.07         0.07         4.14        23.97         9.80        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 
        8.94         3.22         1.38        25.22        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN 
      116.88        13.58        73.28         6.28         3.91        71.70 
TCGA-K1-A3PO TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       36.39        11.70         2.37         0.49         5.69         4.47 
TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
       11.08         0.10         4.08        75.52        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       38.63        81.01        18.08         1.84        46.82        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WD 
       18.18        21.01        13.22         0.72        18.08         8.52 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.10               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             80.48             143.41 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            21.335             16.705 
[1] "0.1 - 80.5 (21.3)"  "0.1 - 143.4 (16.7)"
[1] "hr=" "1.3"
D62V2, continuous
D62V3, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   19 17
  11Q LOSS WILD-TYPE 43 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     19   17
  11Q LOSS WILD-TYPE   43   35
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               19                 43
  MALE                 17                 35
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       1                         2    22
  11Q LOSS WILD-TYPE     3                         6    55
D62V4, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                2                  6
  WHITE                                   22                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED   19  6
  12P LOSS WILD-TYPE 59 30
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                25                 89 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 6                 30 
$`12P LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A3LY 
        2.04        46.68        74.66         8.58         9.70        17.10 
TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A48V 
       14.99        28.80        64.18        24.26        26.47        25.08 
TCGA-DX-A6BA TCGA-DX-A6BF TCGA-FX-A3NJ TCGA-HS-A5N7 TCGA-IE-A4EJ TCGA-IE-A6BZ 
       54.87         2.07         0.10        23.97         3.22         7.13 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-KF-A41W TCGA-MJ-A68H TCGA-PC-A5DM TCGA-SG-A6Z7 
        6.28         1.05        11.70         4.47         6.35         3.88 
TCGA-X6-A7WD 
        8.52 

$`12P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 
       14.04        27.19        12.85        24.49        18.54        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       31.56        29.85         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
       27.81        60.30        53.26        43.04         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       70.49       108.13        20.05        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J 
        4.54        10.68        44.45        39.35        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B9 
       19.30        12.26        27.22        14.96        72.72        11.47 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS 
       10.78        16.31         7.36         1.68        16.18         0.46 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        0.07         0.07        26.89         4.57         4.14        12.62 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
        0.10        41.33         9.80        80.48        21.37         8.94 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        1.38        37.12        25.22        31.76        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A75J 
      116.88        13.58        73.28         5.92        22.62         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       71.70        36.39         5.26         2.37         0.49         5.69 
TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.08         0.10         4.08        75.52        37.55        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       81.01        18.08         1.84        46.82        18.08        18.18 
TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC 
       21.01        13.22         0.72        18.08        27.16 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.10               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             74.66             143.41 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              9.70              18.18 
[1] "0.1 - 74.7 (9.7)"   "0.1 - 143.4 (18.2)"
[1] "hr=" "1.1"
D63V2, continuous
D63V3, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   14 11
  12P LOSS WILD-TYPE 48 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     14   11
  12P LOSS WILD-TYPE   48   41
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               14                 48
  MALE                 11                 41
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         3    16
  12P LOSS WILD-TYPE     4                         5    61
D63V4, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                3                  5
  WHITE                                   16                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED   18  8
  12Q LOSS WILD-TYPE 60 28
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                26                 88 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                 28 
$`12Q LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A2J0 
        2.04        46.68        74.66         6.28         8.58         9.70 
TCGA-DX-A3LS TCGA-DX-A3LY TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A6BA 
        9.04        17.10        64.18        24.26        26.47        54.87 
TCGA-DX-A6BF TCGA-FX-A3NJ TCGA-HS-A5N7 TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A6BZ 
        2.07         0.10        23.97        21.37         3.22         7.13 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-KF-A41W TCGA-MJ-A68H TCGA-PC-A5DM TCGA-PC-A5DO 
        6.28         1.05        11.70         4.47         6.35        81.01 
TCGA-SG-A6Z7 TCGA-X6-A7WD 
        3.88         8.52 

$`12Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 
       14.04        27.19        12.85        24.49        18.54        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       31.56        29.85         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       60.30        53.26        43.04        23.08        70.49       108.13 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       20.05        15.06        17.75        42.77         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       10.68        44.45        39.35        28.80        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V 
       19.30        12.26        27.22        14.96        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       11.47        10.78        16.31         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z 
        0.46         0.07         0.07        26.89         4.57         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
       12.62         0.10        41.33         9.80        80.48         8.94 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        1.38        37.12        25.22        31.76        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A75J 
      116.88        13.58        73.28         5.92        22.62         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       71.70        36.39         5.26         2.37         0.49         5.69 
TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.08         0.10         4.08        75.52        37.55        38.63 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
       18.08         1.84        46.82        18.08        18.18        21.01 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC 
       13.22         0.72        18.08        27.16 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.10               0.07 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             81.01             143.41 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              8.81              18.36 
[1] "0.1 - 81.0 (8.8)"   "0.1 - 143.4 (18.4)"
[1] "hr=" "1.3"
D64V2, continuous
D64V3, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED   17  9
  12Q LOSS WILD-TYPE 45 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     17    9
  12Q LOSS WILD-TYPE   45   43
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               17                 45
  MALE                  9                 43
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       0                         3    16
  12Q LOSS WILD-TYPE     4                         5    61
D64V4, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                3                  5
  WHITE                                   16                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   36 19
  13Q LOSS WILD-TYPE 42 17
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                55                 59 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                19                 17 
$`13Q LOSS MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R 
       14.04        27.19        24.49        18.54        46.68        74.66 
TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 
        6.28         9.70         9.04        23.08        17.10        20.05 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       39.35        28.80        64.18         9.73        19.30        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48V TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BF 
       27.22        14.96        25.08        54.87        10.78         2.07 
TCGA-DX-A6BK TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 
       16.18         0.07         0.07        26.89         4.57        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ 
       23.97         0.10         9.80         3.22         7.13        37.12 
TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
      143.41        73.28        22.62         1.05         3.91        71.70 
TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL 
       11.70         2.37         5.69         0.10         4.08        37.55 
TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-SG-A6Z7 
        6.35        81.01        46.82        18.08        18.18         3.88 
TCGA-X6-A7WC 
       27.16 

$`13Q LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
        2.04        12.85        42.44        31.56        29.85         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 
       76.41        66.87        27.81        60.30         8.58        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       43.04        70.49       108.13        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UE TCGA-DX-A48N 
        4.54        14.99        10.68        44.45        34.88        12.26 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       26.47        72.72        11.47        16.31         7.36         1.68 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EH 
        0.46         0.10         4.14        41.33        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
        8.94         1.38        25.22        31.76        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5YA 
       13.58         5.92         6.28        36.39         5.26         0.49 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 
        4.47        11.08        75.52        38.63        18.08         1.84 
TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WD 
       21.01        13.22         0.72        18.08         8.52 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.07               0.10 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            143.41             116.88 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             18.08              17.75 
[1] "0.1 - 143.4 (18.1)" "0.1 - 116.9 (17.8)"
[1] "hr=" "1.3"
D65V2, continuous
D65V3, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   35 20
  13Q LOSS WILD-TYPE 27 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     35   20
  13Q LOSS WILD-TYPE   27   32
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               35                 27
  MALE                 20                 32
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       2                         4    39
  13Q LOSS WILD-TYPE     2                         4    38
D65V4, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    2                  2
  BLACK OR AFRICAN AMERICAN                4                  4
  WHITE                                   39                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   24  6
  14Q LOSS WILD-TYPE 54 30
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                30                 84 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 6                 30 
$`14Q LOSS MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23R 
       14.04         2.04        27.19        24.49        42.44        74.66 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A48N TCGA-DX-A48O 
       23.08        70.49        17.10        15.06        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48U TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A48G TCGA-HS-A5N8 
       14.96        72.72         0.46         0.10         0.07         0.10 
TCGA-HS-A5NA TCGA-IE-A4EJ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        9.80         3.22        37.12        28.21       143.41       116.88 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-QQ-A5V9 TCGA-X6-A7WB 
       73.28        22.62         6.28         1.05        46.82        18.08 

$`14Q LOSS WILD-TYPE`
TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       12.85        18.54        46.68        31.56        29.85         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3M1 
        9.70        53.26        43.04         9.04       108.13        20.05 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       24.26        26.47        25.08        11.47        54.87        10.78 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A3RE 
       16.31         2.07         7.36         1.68        16.18         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 
       26.89         4.57         4.14        12.62        23.97        41.33 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ 
       80.48        21.37         8.94         1.38         7.13        25.22 
TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       31.76        13.58         5.92         3.91        71.70        36.39 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       11.70         5.26         2.37         0.49         5.69         4.47 
TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
       11.08         0.10         4.08        75.52        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       38.63        81.01        18.08         1.84        18.08        18.18 
TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WC TCGA-X6-A7WD 
       21.01         3.88        13.22         0.72        27.16         8.52 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.07               0.07 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            143.41             108.13 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             20.35              17.03 
[1] "0.1 - 143.4 (20.4)" "0.1 - 108.1 (17.0)"
[1] "hr=" "2.1"
D66V2, continuous
D66V3, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   18 12
  14Q LOSS WILD-TYPE 44 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     18   12
  14Q LOSS WILD-TYPE   44   40
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               18                 44
  MALE                 12                 40
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       1                         2    20
  14Q LOSS WILD-TYPE     3                         6    57
D66V4, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                2                  6
  WHITE                                   20                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    9  8
  15Q LOSS WILD-TYPE 69 28
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                17                 97 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 8                 28 
$`15Q LOSS MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3UA TCGA-DX-A3UB 
       14.04         2.04         9.04        23.08        10.68        44.45 
TCGA-DX-A48R TCGA-DX-A6BF TCGA-FX-A48G TCGA-HB-A3YV TCGA-IF-A3RQ TCGA-IS-A3K7 
       26.47         2.07         0.07         4.57        37.12       143.41 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-KF-A41W TCGA-PC-A5DM TCGA-X6-A7WB 
        5.92         6.28        11.70         6.35        18.08 

$`15Q LOSS WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       27.19        12.85        24.49        18.54        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        29.85        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       43.04        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD 
       17.75        42.77         4.54        14.99        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       27.22        14.96        72.72        25.08        11.47        54.87 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS 
       10.78        16.31         7.36         1.68        16.18         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.10         0.07        26.89         4.14        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
        0.10        41.33         9.80        80.48        21.37         8.94 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        3.22         1.38         7.13        25.22        31.76        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J 
      116.88        13.58        73.28        22.62         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       71.70        36.39         5.26         2.37         0.49         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
        4.47        11.08         0.10         4.08        75.52        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       38.63        81.01        18.08         1.84        46.82        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WC 
       18.18        21.01         3.88        13.22         0.72        27.16 
TCGA-X6-A7WD 
        8.52 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.07               0.07 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            143.41             116.88 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             10.68              18.18 
[1] "0.1 - 143.4 (10.7)" "0.1 - 116.9 (18.2)"
[1] "hr=" "2.2"
D67V2, continuous
D67V3, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   10  7
  15Q LOSS WILD-TYPE 52 45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     10    7
  15Q LOSS WILD-TYPE   52   45
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               10                 52
  MALE                  7                 45
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       0                         1    15
  15Q LOSS WILD-TYPE     4                         7    62
D67V4, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                1                  7
  WHITE                                   15                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED   25  8
  16P LOSS WILD-TYPE 53 28
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                33                 81 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 8                 28 
$`16P LOSS MUTATED`
TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LT TCGA-DX-A3U7 
       18.54        42.44        74.66         6.28        23.08        42.77 
TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48O TCGA-DX-A6BA TCGA-FX-A3RE 
       10.68        28.80        64.18        27.22        54.87         0.07 
TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-IE-A4EJ TCGA-IE-A6BZ 
        0.07         4.57         4.14         0.10         3.22         7.13 
TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-KF-A41W 
       37.12       143.41         6.28         1.05        71.70        11.70 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-N1-A6IA TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD 
        5.69         4.47         4.08        46.82        18.18        21.01 
TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WD 
        0.72        18.08         8.52 

$`16P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       14.04         2.04        27.19        12.85        24.49        46.68 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       31.56        29.85         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        53.26        43.04         9.04 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J 
        4.54        14.99        44.45        39.35        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       19.30        24.26        12.26        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       25.08        11.47        10.78        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-HB-A2OT TCGA-HB-A5W3 
        1.68        16.18         0.46         0.10        26.89        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
       23.97        41.33         9.80        80.48        21.37         8.94 
TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA 
        1.38        25.22        31.76        28.21       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A75J TCGA-K1-A3PO TCGA-LI-A67I 
       73.28         5.92        22.62         3.91        36.39         5.26 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68J TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL 
        2.37         0.49        11.08         0.10        75.52        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA 
        6.35        38.63        81.01        18.08         1.84        18.08 
TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WC 
        3.88        13.22        27.16 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.07               0.10 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            143.41             116.88 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             11.70              18.08 
[1] "0.1 - 143.4 (11.7)" "0.1 - 116.9 (18.1)"
[1] "hr=" "1.2"
D68V2, continuous
D68V3, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   24  9
  16P LOSS WILD-TYPE 38 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     24    9
  16P LOSS WILD-TYPE   38   43
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               24                 38
  MALE                  9                 43
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       1                         4    23
  16P LOSS WILD-TYPE     3                         4    54
D68V4, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                4                  4
  WHITE                                   23                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   41 18
  16Q LOSS WILD-TYPE 37 18
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                59                 55 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                18                 18 
$`16Q LOSS MUTATED`
TCGA-DX-A1KU TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 
       14.04        18.54        42.44        74.66         6.28         9.70 
TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC 
       23.08        17.10        42.77        14.99        10.68        39.35 
TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       28.80        64.18        19.30        24.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6BA TCGA-DX-A6BB TCGA-FX-A3NJ TCGA-FX-A3RE 
       26.47        25.08        54.87        10.78         0.10         0.07 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07        26.89         4.57         4.14        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        0.10         9.80        21.37         8.94         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M4 
        7.13        37.12        25.22        31.76        13.58        73.28 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-KF-A41W TCGA-MB-A8JL TCGA-MJ-A68H 
        6.28         1.05        71.70        11.70         5.69         4.47 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V9 
        0.10         4.08        37.55        81.01        18.08        46.82 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WD 
       18.18        21.01         0.72        18.08         8.52 

$`16Q LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 
        2.04        27.19        12.85        24.49        46.68        31.56 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       29.85         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        8.58        53.26        43.04         9.04        70.49       108.13 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UE 
       20.05        15.06        17.75         4.54        44.45        34.88 
TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF 
        9.73        12.26        72.72        11.47        16.31         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-HS-A5N9 TCGA-IE-A3OV 
        7.36         1.68        16.18         0.46        41.33        80.48 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A75J 
       28.21       143.41       116.88         5.92        22.62         3.91 
TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68J TCGA-PC-A5DK 
       36.39         5.26         2.37         0.49        11.08        75.52 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-SG-A6Z7 TCGA-UE-A6QT 
        6.35        38.63         1.84        18.08         3.88        13.22 
TCGA-X6-A7WC 
       27.16 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.07               0.46 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             81.01             143.41 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             17.10              18.08 
[1] "0.1 - 81.0 (17.1)"  "0.5 - 143.4 (18.1)"
[1] "hr=" "1.2"
D69V2, continuous
D69V3, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   38 21
  16Q LOSS WILD-TYPE 24 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     38   21
  16Q LOSS WILD-TYPE   24   31
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               38                 24
  MALE                 21                 31
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       2                         5    44
  16Q LOSS WILD-TYPE     2                         3    33
D69V4, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    2                  2
  BLACK OR AFRICAN AMERICAN                5                  3
  WHITE                                   44                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   14  8
  17P LOSS WILD-TYPE 64 28
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                22                 92 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 8                 28 
$`17P LOSS MUTATED`
TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A6BB 
       24.49        74.66        23.08        14.99        10.68        10.78 
TCGA-FX-A3NJ TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EJ 
        0.10        26.89         0.10        41.33        80.48         3.22 
TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-KF-A41W TCGA-MB-A5YA 
        1.38        25.22        28.21       143.41        11.70         0.49 
TCGA-PC-A5DL TCGA-PC-A5DP TCGA-QQ-A5VC TCGA-SG-A6Z7 
       37.55        18.08        18.18         3.88 

$`17P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        27.19        12.85        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       42.44        31.56        29.85         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       43.04         9.04        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC 
       15.06        17.75        42.77         4.54        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       28.80        34.88        64.18         9.73        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       11.47        54.87        16.31         2.07         7.36         1.68 
TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A43Z 
       16.18         0.46         0.07         0.07         4.57         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A6BZ 
       12.62        23.97         9.80        21.37         8.94         7.13 
TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       37.12        31.76       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       22.62         6.28         1.05         3.91        71.70        36.39 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
        5.26         2.37         5.69         4.47        11.08         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 
        4.08        75.52         6.35        38.63        81.01         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB 
       46.82        18.08        21.01        13.22         0.72        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD 
       27.16         8.52 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.10               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            143.41             116.88 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            18.130             17.425 
[1] "0.1 - 143.4 (18.1)" "0.1 - 116.9 (17.4)"
[1] "hr=" "1.1"
D70V2, continuous
D70V3, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   12 10
  17P LOSS WILD-TYPE 50 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     12   10
  17P LOSS WILD-TYPE   50   42
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               12                 50
  MALE                 10                 42
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       0                         1    17
  17P LOSS WILD-TYPE     4                         7    60
D70V4, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                1                  7
  WHITE                                   17                 60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED   12 10
  17Q LOSS WILD-TYPE 66 26
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                22                 92 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                10                 26 
$`17Q LOSS MUTATED`
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LT TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UD 
       74.66         6.28        23.08        14.99        10.68        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6BA TCGA-FX-A3NJ TCGA-HB-A2OT 
       34.88        64.18        24.26        54.87         0.10        26.89 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-KF-A41W 
        0.10        41.33        80.48         3.22        25.22        11.70 
TCGA-PC-A5DL TCGA-PC-A5DP TCGA-SG-A6Z7 TCGA-X6-A7WC 
       37.55        18.08         3.88        27.16 

$`17Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       46.68        42.44        31.56        29.85         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87        27.81        60.30         8.58         9.70        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       43.04         9.04        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC 
       15.06        17.75        42.77         4.54        44.45        39.35 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        19.30        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       72.72        25.08        11.47        10.78        16.31         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A48G 
        7.36         1.68        16.18         0.46         0.07         0.07 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EH 
        4.57         4.14        12.62        23.97         9.80        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 
        8.94         1.38         7.13        37.12        31.76        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
      143.41       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I 
        6.28         1.05         3.91        71.70        36.39         5.26 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
        2.37         0.49         5.69         4.47        11.08         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 
        4.08        75.52         6.35        38.63        81.01         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU 
       46.82        18.08        18.18        21.01        13.22         0.72 
TCGA-X6-A7WB TCGA-X6-A7WD 
       18.08         8.52 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.10               0.07 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             80.48             143.41 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            24.740             16.245 
[1] "0.1 - 80.5 (24.7)"  "0.1 - 143.4 (16.2)"
[1] "hr=" "1.5"
D71V2, continuous
D71V3, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   13  9
  17Q LOSS WILD-TYPE 49 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     13    9
  17Q LOSS WILD-TYPE   49   43
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               13                 49
  MALE                  9                 43
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         1    17
  17Q LOSS WILD-TYPE     4                         7    60
D71V4, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                1                  7
  WHITE                                   17                 60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   15 12
  18P LOSS WILD-TYPE 63 24
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                27                 87 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                12                 24 
$`18P LOSS MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LT 
       27.19        12.85        18.54         6.28         9.70        23.08 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48P TCGA-DX-A6BF 
       14.99        10.68        39.35        64.18        14.96         2.07 
TCGA-HB-A2OT TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IS-A3K7 
       26.89        23.97        80.48        21.37         3.22       143.41 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-KF-A41W TCGA-MJ-A68H TCGA-PC-A5DL 
       73.28        22.62         1.05        11.70         4.47        37.55 
TCGA-PC-A5DP TCGA-SG-A6Z7 TCGA-X6-A7WB 
       18.08         3.88        18.08 

$`18P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04         2.04        24.49        46.68        42.44        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       29.85        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
       60.30         8.58        53.26        43.04         9.04        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
      108.13        17.10        20.05        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
        4.54        44.45        28.80        34.88         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       24.26        12.26        27.22        26.47        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       11.47        54.87        10.78        16.31         7.36         1.68 
TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV 
       16.18         0.46         0.10         0.07         0.07         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EI 
        4.14        12.62         0.10        41.33         9.80         8.94 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        1.38         7.13        37.12        25.22        31.76        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN 
      116.88        13.58         5.92         6.28         3.91        71.70 
TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J 
       36.39         5.26         2.37         0.49         5.69        11.08 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
        0.10         4.08        75.52         6.35        38.63        81.01 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT 
        1.84        46.82        18.08        18.18        21.01        13.22 
TCGA-UE-A6QU TCGA-X6-A7WC TCGA-X6-A7WD 
        0.72        27.16         8.52 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              1.05               0.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            143.41             116.88 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             18.08              17.10 
[1] "1.1 - 143.4 (18.1)" "0.1 - 116.9 (17.1)"
[1] "hr=" "1.6"
D72V2, continuous
D72V3, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   19  8
  18P LOSS WILD-TYPE 43 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     19    8
  18P LOSS WILD-TYPE   43   44
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               19                 43
  MALE                  8                 44
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       1                         3    17
  18P LOSS WILD-TYPE     3                         5    60
D72V4, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                3                  5
  WHITE                                   17                 60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   16 12
  18Q LOSS WILD-TYPE 62 24
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                28                 86 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                12                 24 
$`18Q LOSS MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LT 
       27.19        12.85        18.54         6.28         9.70        23.08 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48P TCGA-DX-A6BA 
       14.99        10.68        64.18        19.30        14.96        54.87 
TCGA-DX-A6BF TCGA-FX-A48G TCGA-HB-A2OT TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IE-A4EJ 
        2.07         0.07        26.89        23.97        80.48         3.22 
TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-KF-A41W TCGA-LI-A67I 
       25.22       143.41        22.62         1.05        11.70         5.26 
TCGA-MJ-A68H TCGA-PC-A5DM TCGA-PC-A5DP TCGA-SG-A6Z7 
        4.47         6.35        18.08         3.88 

$`18Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04         2.04        24.49        46.68        42.44        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       29.85        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
       60.30         8.58        53.26        43.04         9.04        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
      108.13        17.10        20.05        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
        4.54        44.45        39.35        28.80        34.88         9.73 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       24.26        12.26        27.22        26.47        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       11.47        10.78        16.31         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        0.46         0.10         0.07         4.57         4.14        12.62 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK 
        0.10        41.33         9.80        21.37         8.94         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA 
        7.13        37.12        31.76        28.21       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       73.28         5.92         6.28         3.91        71.70        36.39 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA 
        2.37         0.49         5.69        11.08         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       75.52        37.55        38.63        81.01         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB 
       18.08        18.18        21.01        13.22         0.72        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD 
       27.16         8.52 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.07               0.07 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            143.41             116.88 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            14.975             18.080 
[1] "0.1 - 143.4 (15.0)" "0.1 - 116.9 (18.1)"
[1] "hr=" "1.8"
D73V2, continuous
D73V3, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   18 10
  18Q LOSS WILD-TYPE 44 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     18   10
  18Q LOSS WILD-TYPE   44   42
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               18                 44
  MALE                 10                 42
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       1                         3    18
  18Q LOSS WILD-TYPE     3                         5    59
D73V4, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                3                  5
  WHITE                                   18                 59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    4  3
  19P LOSS WILD-TYPE 74 33
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 7                107 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 33 
$`19P LOSS MUTATED`
TCGA-DX-A3LT TCGA-IE-A4EH TCGA-IW-A3M6 TCGA-LI-A67I TCGA-PC-A5DM TCGA-PC-A5DO 
       23.08        21.37        22.62         5.26         6.35        81.01 
TCGA-SG-A6Z7 
        3.88 

$`19P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        42.44        31.56        29.85        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        9.70        53.26        43.04         9.04        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       17.10        20.05        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       64.18         9.73        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        26.47        72.72        25.08        11.47        54.87 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       10.78        16.31         2.07         7.36         1.68        16.18 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV 
        0.46         0.10         0.07         0.07        26.89         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.14        12.62        23.97         0.10        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       80.48         8.94         3.22         1.38         7.13        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        31.76        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       73.28         5.92         6.28         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       36.39        11.70         2.37         0.49         5.69         4.47 
TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.08         0.10         4.08        75.52        37.55        38.63 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
       18.08         1.84        46.82        18.08        18.18        21.01 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       13.22         0.72        18.08        27.16         8.52 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              3.88               0.07 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             81.01             143.41 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             21.37              17.75 
[1] "3.9 - 81.0 (21.4)"  "0.1 - 143.4 (17.8)"
[1] "hr=" "1.3"
D74V2, continuous
D74V3, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    5  2
  19P LOSS WILD-TYPE 57 50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      5    2
  19P LOSS WILD-TYPE   57   50
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                5                 57
  MALE                  2                 50
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       1                         0     6
  19P LOSS WILD-TYPE     3                         8    71
D74V4, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                0                  8
  WHITE                                    6                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    9  8
  19Q LOSS WILD-TYPE 69 28
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                17                 97 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 8                 28 
$`19Q LOSS MUTATED`
TCGA-DX-A1L0 TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3UD TCGA-FX-A48G 
       18.54         9.70        23.08        42.77        28.80         0.07 
TCGA-HB-A3YV TCGA-IE-A4EH TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A75J TCGA-LI-A67I 
        4.57        21.37        73.28        22.62         3.91         5.26 
TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DO TCGA-SG-A6Z7 TCGA-X6-A7WB 
       75.52         6.35        81.01         3.88        18.08 

$`19Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       14.04         2.04        27.19        12.85        24.49        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       42.44        31.56        29.85        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 
       66.87         6.28        27.81        60.30         8.58        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       43.04         9.04        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       15.06        17.75         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       39.35        34.88        64.18         9.73        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        54.87        10.78        16.31         2.07         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A2OT 
        1.68        16.18         0.46         0.10         0.07        26.89 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.14        12.62        23.97         0.10        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       80.48         8.94         3.22         1.38         7.13        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        31.76        28.21       143.41       116.88        13.58 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W 
        5.92         6.28         1.05        71.70        36.39        11.70 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
        2.37         0.49         5.69         4.47        11.08         0.10 
TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 
        4.08        37.55        38.63        18.08         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WC 
       18.08        18.18        21.01        13.22         0.72        27.16 
TCGA-X6-A7WD 
        8.52 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.07               0.07 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             81.01             143.41 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             18.54              17.10 
[1] "0.1 - 81.0 (18.5)"  "0.1 - 143.4 (17.1)"
[1] "hr=" "1.6"
D75V2, continuous
D75V3, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    9  8
  19Q LOSS WILD-TYPE 53 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      9    8
  19Q LOSS WILD-TYPE   53   44
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                9                 53
  MALE                  8                 44
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       1                         0    14
  19Q LOSS WILD-TYPE     3                         8    63
D75V4, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                0                  8
  WHITE                                   14                 63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED   12  6
  20P LOSS WILD-TYPE 66 30
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                 96 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 6                 30 
$`20P LOSS MUTATED`
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A3UE 
        9.04        23.08        17.10        20.05        14.99        34.88 
TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48V TCGA-FX-A2QS TCGA-IE-A6BZ 
       64.18        19.30        24.26        25.08         0.46         7.13 
TCGA-JV-A5VE TCGA-K1-A3PN TCGA-PC-A5DK TCGA-PC-A5DO TCGA-QQ-A5VC TCGA-X6-A7WB 
        6.28        71.70        75.52        81.01        18.18        18.08 

$`20P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        42.44        31.56        29.85        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 
        9.70        53.26        43.04        70.49       108.13        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75        42.77         4.54        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       28.80         9.73        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       72.72        11.47        54.87        10.78        16.31         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
        7.36         1.68        16.18         0.10         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       26.89         4.57         4.14        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
       41.33         9.80        80.48        21.37         8.94         3.22 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        1.38        37.12        25.22        31.76        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF 
      116.88        13.58        73.28         5.92        22.62         1.05 
TCGA-JV-A75J TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA 
        3.91        36.39        11.70         5.26         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL 
        5.69         4.47        11.08         0.10         4.08        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
        6.35        38.63        18.08         1.84        46.82        18.08 
TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WC TCGA-X6-A7WD 
       21.01         3.88        13.22         0.72        27.16         8.52 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.46               0.07 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             81.01             143.41 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            19.675             15.620 
[1] "0.5 - 81.0 (19.7)"  "0.1 - 143.4 (15.6)"
[1] "hr=" "1.1"
D76V2, continuous
D76V3, binary
                    cls
clus                  0  1
  20P LOSS MUTATED   11  7
  20P LOSS WILD-TYPE 51 45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     11    7
  20P LOSS WILD-TYPE   51   45
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               11                 51
  MALE                  7                 45
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         1    17
  20P LOSS WILD-TYPE     4                         7    60
D76V4, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                1                  7
  WHITE                                   17                 60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                 0  1
  20Q LOSS MUTATED    5  3
  20Q LOSS WILD-TYPE 73 33
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                106 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 33 
$`20Q LOSS MUTATED`
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A3UE 
        9.04        23.08        17.10        20.05        14.99        34.88 
TCGA-IE-A6BZ TCGA-JV-A5VE 
        7.13         6.28 

$`20Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        27.19        12.85        24.49        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        42.44        31.56        29.85        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 
        9.70        53.26        43.04        70.49       108.13        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75        42.77         4.54        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       28.80        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 
       27.22        14.96        26.47        72.72        25.08        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       54.87        10.78        16.31         2.07         7.36         1.68 
TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
       16.18         0.46         0.10         0.07         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
        4.57         4.14        12.62        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37         8.94         3.22         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       37.12        25.22        31.76        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        73.28         5.92        22.62         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA 
       71.70        36.39        11.70         5.26         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
        5.69         4.47        11.08         0.10         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 
       37.55         6.35        38.63        81.01        18.08         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT 
       46.82        18.08        18.18        21.01         3.88        13.22 
TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        0.72        18.08        27.16         8.52 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              6.28               0.07 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             34.88             143.41 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            16.045             18.080 
[1] "6.3 - 34.9 (16.0)"  "0.1 - 143.4 (18.1)"
[1] "hr=" "1.7"
D77V2, continuous
D77V3, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    4  4
  20Q LOSS WILD-TYPE 58 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4    4
  20Q LOSS WILD-TYPE   58   48
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                4                 58
  MALE                  4                 48
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         1     7
  20Q LOSS WILD-TYPE     4                         7    70
D77V4, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                1                  7
  WHITE                                    7                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   15  4
  21Q LOSS WILD-TYPE 63 32
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                19                 95 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 4                 32 
$`21Q LOSS MUTATED`
TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LY 
       27.19        18.54        42.44        74.66         6.28        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3UF TCGA-DX-A6BB TCGA-DX-A6BF TCGA-HB-A2OT 
       20.05        15.06        64.18        10.78         2.07        26.89 
TCGA-IS-A3K7 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-KF-A41W TCGA-PC-A5DO 
      143.41        22.62         6.28        71.70        11.70        81.01 
TCGA-SG-A6Z7 
        3.88 

$`21Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 
       14.04         2.04        12.85        24.49        46.68        31.56 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       29.85         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        53.26        43.04         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       70.49       108.13        17.75        42.77         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       10.68        44.45        39.35        28.80        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       19.30        24.26        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BG 
       72.72        25.08        11.47        54.87        16.31         7.36 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
        1.68        16.18         0.46         0.10         0.07         0.07 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
        4.57         4.14        12.62        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37         8.94         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
        7.13        37.12        25.22        31.76        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO 
       13.58        73.28         5.92         1.05         3.91        36.39 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        5.26         2.37         0.49         5.69         4.47        11.08 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
        0.10         4.08        75.52        37.55         6.35        38.63 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
       18.08         1.84        46.82        18.08        18.18        21.01 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       13.22         0.72        18.08        27.16         8.52 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              2.07               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            143.41             116.88 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             20.05              16.31 
[1] "2.1 - 143.4 (20.1)" "0.1 - 116.9 (16.3)"
[1] "hr=" "2.3"
D78V2, continuous
D78V3, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   12  7
  21Q LOSS WILD-TYPE 50 45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     12    7
  21Q LOSS WILD-TYPE   50   45
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               12                 50
  MALE                  7                 45
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       1                         2    11
  21Q LOSS WILD-TYPE     3                         6    66
D78V4, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                2                  6
  WHITE                                   11                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   21 12
  22Q LOSS WILD-TYPE 57 24
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                33                 81 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                12                 24 
$`22Q LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A2IZ 
        2.04        46.68        42.44        66.87         6.28         8.58 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A48L 
        9.04        23.08       108.13        20.05        14.99        24.26 
TCGA-DX-A48R TCGA-DX-A6BA TCGA-DX-A6BK TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV 
       26.47        54.87        16.18         0.07         0.07         4.57 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 
        0.10         9.80        21.37         7.13        25.22       143.41 
TCGA-IS-A3K8 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A3PN TCGA-KF-A41W 
      116.88         5.92        22.62         1.05        71.70        11.70 
TCGA-LI-A67I TCGA-SG-A6Z7 TCGA-X6-A7WB 
        5.26         3.88        18.08 

$`22Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 
       14.04        27.19        12.85        24.49        18.54        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23Z TCGA-DX-A240 
       29.85        74.66         5.26        76.41        27.81        60.30 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 
        9.70        53.26        43.04        70.49        17.10        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75        42.77         4.54        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N 
       28.80        34.88        64.18         9.73        19.30        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BB 
       27.22        14.96        72.72        25.08        11.47        10.78 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS TCGA-FX-A3NJ 
       16.31         2.07         7.36         1.68         0.46         0.10 
TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-IE-A3OV 
       26.89         4.14        12.62        23.97        41.33        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 
        8.94         3.22         1.38        37.12        31.76        28.21 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PO TCGA-MB-A5Y9 
       13.58        73.28         6.28         3.91        36.39         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA 
        0.49         5.69         4.47        11.08         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
       75.52        37.55         6.35        38.63        81.01        18.08 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT 
        1.84        46.82        18.08        18.18        21.01        13.22 
TCGA-UE-A6QU TCGA-X6-A7WC TCGA-X6-A7WD 
        0.72        27.16         8.52 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.07               0.10 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            143.41              81.01 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             16.18              18.08 
[1] "0.1 - 143.4 (16.2)" "0.1 - 81.0 (18.1)" 
[1] "hr=" "1.1"
D79V2, continuous
D79V3, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   21 12
  22Q LOSS WILD-TYPE 41 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     21   12
  22Q LOSS WILD-TYPE   41   40
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               21                 41
  MALE                 12                 40
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       1                         1    23
  22Q LOSS WILD-TYPE     3                         7    54
D79V4, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                1                  7
  WHITE                                   23                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   28 14
  XQ LOSS WILD-TYPE 50 22
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               42                72 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               14                22 
$`XQ LOSS MUTATED`
TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A2J0 TCGA-DX-A3LY 
       12.85        18.54        42.44        74.66         9.70        17.10 
TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       20.05        10.68        39.35        28.80        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
        9.73        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A5W3 
       11.47        54.87        10.78         0.07         4.57        12.62 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 
       23.97         9.80        21.37        37.12        25.22        28.21 
TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-MB-A8JL TCGA-MJ-A68H 
      143.41        73.28        22.62         6.28         5.69         4.47 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5VC TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WD 
       38.63        81.01        18.18         0.72        18.08         8.52 

$`XQ LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 
       14.04         2.04        27.19        24.49        46.68        31.56 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       29.85         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
       60.30         8.58        53.26        43.04         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       70.49       108.13        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A6BE 
       14.99        44.45        19.30        24.26        12.26        16.31 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ 
        2.07         7.36         1.68        16.18         0.46         0.10 
TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV 
        0.07        26.89         4.14         0.10        41.33        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-IS-A3K8 
        8.94         3.22         1.38         7.13        31.76       116.88 
TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       13.58         5.92         1.05         3.91        71.70        36.39 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68J TCGA-MO-A47R 
       11.70         5.26         2.37         0.49        11.08         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A5V2 
        4.08        75.52        37.55         6.35        18.08         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-X6-A7WC 
       46.82        18.08        21.01         3.88        13.22        27.16 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.07              0.07 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           143.41            116.88 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           20.710            15.025 
[1] "0.1 - 143.4 (20.7)" "0.1 - 116.9 (15.0)"
[1] "hr=" "1.1"
D80V2, continuous
D80V3, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   28 14
  XQ LOSS WILD-TYPE 34 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     28   14
  XQ LOSS WILD-TYPE   34   38
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              28                34
  MALE                14                38
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       2                         4    29
  XQ LOSS WILD-TYPE     2                         4    48
D80V4, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   2                 2
  BLACK OR AFRICAN AMERICAN               4                 4
  WHITE                                  29                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"
