[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"        "-oTPCPG-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/PCPG-TP/11541607/PCPG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PCPG-TP/11548820/transformed.cor.cli.txt"

nPatients in clinical file=132, in cluster file=162, common to both=129
[1] "Reduce the number of clustering variables from 80 to 63."
[1]  63 129
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6               123 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6               123 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               15               114 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               15               114 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                3               126 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                3               126 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3               126 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3               126 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               126 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               126 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                9               120 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                9               120 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6               123 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6               123 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               10               119 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               10               119 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4               125 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4               125 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               22               107 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               22               107 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               18               111 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               18               111 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7               122 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7               122 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               10               119 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               10               119 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               126 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               126 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 9                120 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 9                120 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                121 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                121 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                124 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                124 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                122 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                122 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                10                119 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                10                119 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 7                122 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 7                122 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                119 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                119 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                124 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                124 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 4                125 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 4                125 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 4                125 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 4                125 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                125 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                125 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 7                122 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 7                122 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                16                113 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                16                113 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                11                118 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                11                118 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                10                119 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                10                119 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 7                122 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 7                122 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4               125 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4               125 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               78                51 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               78                51 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               17               112 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               17               112 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                7               122 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                7               122 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                8               121 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                8               121 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               47                82 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               47                82 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               70                59 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               70                59 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                8               121 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                8               121 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                8               121 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                8               121 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4               125 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4               125 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6               123 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6               123 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               16               113 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               16               113 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               125 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               125 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               15               114 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               15               114 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               120 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               120 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                7               122 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                7               122 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                8               121 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                8               121 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                41                 88 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                41                 88 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                34                 95 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                34                 95 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 6                123 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 6                123 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                16                113 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                16                113 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 3                126 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 3                126 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                123 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                123 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                125 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                125 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                50                 79 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                50                 79 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                16                113 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                16                113 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                10                119 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                10                119 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 3                126 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 3                126 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                125 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                125 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                126 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                126 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                30                 99 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                30                 99 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                47                 82 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                47                 82 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               38                91 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               38                91 
[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 129 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
         957          883           69           29          179          240 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
        2485          852           38         1102          211           55 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
          22          766           70          134           24           29 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
        1178           28         2957         1249          246         2643 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
         604           89          216         1013          724           32 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
          26          405           37          356          397          242 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 
         191         2214          457           21          134           54 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
          NA           18          611          730          800          715 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
         441          346          909          912          601          527 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC 
         324          358          185          240          371         3180 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
        3087         2149         2040         2983          274         3013 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT 
          43            3         1558         1656         2222         3247 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
        3362         3269           NA          750          345         1509 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
         132          765          242          317          770          432 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
         522           36          604          366          380          505 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
         538          779          324          840          678          136 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
         144          128         9219         3880          887           NA 
TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
        1000          182          531          992          795          234 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
         371           24         1131          730          737         1294 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
          34           57          595          652         1406          395 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
          NA           49          357          288         2161         1719 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
          41         2822          210 
Variable 1:'AGE':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=116,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'BATCH.NUMBER':	nDistinctValues=2,	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 129 columns, 1 survival variables, and 3 non-survival variables.
AGE, nv=56, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED     6   0
  1P GAIN WILD-TYPE 119   4
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6               123 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                0                 4 
$`1P GAIN MUTATED`
TCGA-RW-A681 TCGA-S7-A7WL TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SR-A6MV TCGA-WB-A81J 
       23.80        20.09       104.55       101.49       107.47         1.87 

$`1P GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 
       19.86         2.93         7.10        33.30         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
       13.32         1.22        11.70        13.05         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02         0.69         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
        0.59        24.00        26.30        23.51        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       29.88        29.98        19.76        17.33        10.65        11.77 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
        6.08         7.89        12.20        70.65        67.07        98.07 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
        9.01        99.06         1.41         0.10        51.22        54.44 
TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
       73.05       106.75       110.53         3.12        24.66        11.34 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15         7.96        10.42        25.32 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD 
       14.20        17.16         1.18        19.86        12.03        12.49 
TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L 
       16.60        17.69        25.61        10.65        27.62        22.29 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       303.09       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 
       19.59        32.88         5.98        17.46        32.61        26.14 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
        7.69        12.20         0.79        37.18        24.00        24.23 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       42.54         1.12        19.56        21.44        46.22        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        11.74         9.47        71.05        56.52 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        1.35        92.78         6.90 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             1.87              0.10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           107.47            303.09 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           62.645            14.200 
[1] "1.9 - 107.5 (62.6)" "0.1 - 303.1 (14.2)"
[1] "hr="     "7.3e+07"
D1V2, continuous
D1V3, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    1  5
  1P GAIN WILD-TYPE 72 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    5
  1P GAIN WILD-TYPE   72   51
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               1                72
  MALE                 5                51
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     0
  1P GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           0     5
  1P GAIN WILD-TYPE                         9   107
D1V4, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      0                 9
  WHITE                                          5               107
[1] 4 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    14   1
  1Q GAIN WILD-TYPE 111   3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               15               114 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                1                 3 
$`1Q GAIN MUTATED`
TCGA-P7-A5NY TCGA-RW-A680 TCGA-RW-A681 TCGA-S7-A7WL TCGA-SP-A6QC TCGA-SP-A6QD 
       31.46        33.30        23.80        20.09       104.55       101.49 
TCGA-SR-A6MV TCGA-SR-A6MZ TCGA-WB-A80P TCGA-WB-A815 TCGA-WB-A819 TCGA-WB-A81G 
      107.47        11.34       303.09         5.98         7.69        24.23 
TCGA-WB-A81J TCGA-WB-A81Q TCGA-WB-A81W 
        1.87        24.82        56.52 

$`1Q GAIN WILD-TYPE`
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       29.03         2.27         0.95         5.88         7.89        81.70 
TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       28.01         1.25        36.23         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
       25.18         2.30         4.41         0.79         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92        97.22        41.06         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
        2.93         7.10         1.05         0.85        13.32         1.22 
TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F 
       11.70        13.05         7.96         6.28        72.79        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WM 
        0.69         4.41         1.78         2.89         0.59        24.00 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       26.30        23.51        14.50        11.38        29.88        29.98 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 
       19.76        17.33        10.65        11.77         6.08         7.89 
TCGA-S7-A7X2 TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
       12.20        70.65        67.07        98.07         9.01        99.06 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT 
        1.41         0.10        51.22        54.44        73.05       106.75 
TCGA-SR-A6MU TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
      110.53         3.12        24.66        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
        7.96        10.42        25.32        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       19.86        12.03        12.49        16.60        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       10.65        27.62        22.29         4.47         4.73         4.21 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A817 
      127.56        29.16        19.59        32.88        17.46        32.61 
TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81H 
       26.14        12.20         0.79        37.18        24.00        42.54 
TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R 
        1.12        19.56        21.44        46.22        12.99         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       11.74         9.47        71.05         1.35        92.78         6.90 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             1.87              0.10 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           303.09            127.56 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           24.820            13.185 
[1] "1.9 - 303.1 (24.8)" "0.1 - 127.6 (13.2)"
[1] "hr=" "1.8"
D2V2, continuous
D2V3, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    5 10
  1Q GAIN WILD-TYPE 68 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5   10
  1Q GAIN WILD-TYPE   68   46
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               5                68
  MALE                10                46
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  0     0
  1Q GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                           0    14
  1Q GAIN WILD-TYPE                         9    98
D2V4, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      0                 9
  WHITE                                         14                98
[1] 4 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     3   0
  2P GAIN WILD-TYPE 122   4
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                3               126 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                0                 4 
$`2P GAIN MUTATED`
TCGA-RW-A68D TCGA-RW-A68F TCGA-WB-A81D 
       72.79        15.02         0.79 

$`2P GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       19.86         2.93         7.10        33.30        23.80         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        0.85        13.32         1.22        11.70        13.05         7.96 
TCGA-RW-A68C TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
        6.28         0.69         4.41         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       20.09        24.00        26.30        23.51        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       29.88        29.98        19.76        17.33        10.65        11.77 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
        6.08         7.89        12.20       104.55       101.49        70.65 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.07        98.07         9.01        99.06         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
       51.22        54.44        73.05       106.75       110.53       107.47 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        11.34        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
        7.96        10.42        25.32        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       19.86        12.03        12.49        16.60        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       10.65        27.62        22.29         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      303.09       127.56        29.16        19.59        32.88         5.98 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81E 
       17.46        32.61        26.14         7.69        12.20        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       21.44        46.22        12.99        24.82         1.61        11.74 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        9.47        71.05        56.52         1.35        92.78         6.90 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.79              0.10 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            72.79            303.09 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            15.02             15.55 
[1] "0.8 - 72.8 (15.0)"  "0.1 - 303.1 (15.6)"
[1] "hr="     "9200000"
D3V2, continuous
D3V3, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    3  0
  2P GAIN WILD-TYPE 70 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3    0
  2P GAIN WILD-TYPE   70   56
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               3                70
  MALE                 0                56
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  0     1
  2P GAIN WILD-TYPE                                1     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                           0     2
  2P GAIN WILD-TYPE                         9   110
D3V4, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                      0                 9
  WHITE                                          2               110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = 4P GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     3   0
  4P GAIN WILD-TYPE 122   4
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3               126 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                0                 4 
$`4P GAIN MUTATED`
TCGA-RW-A68D TCGA-SP-A6QI TCGA-WB-A80K 
       72.79        98.07        27.62 

$`4P GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       19.86         2.93         7.10        33.30        23.80         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        0.85        13.32         1.22        11.70        13.05         7.96 
TCGA-RW-A68C TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
        6.28        15.02         0.69         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        0.59        20.09        24.00        26.30        23.51        14.50 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       11.38        29.88        29.98        19.76        17.33        10.65 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD 
       11.77         6.08         7.89        12.20       104.55       101.49 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       70.65        67.07         9.01        99.06         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
       51.22        54.44        73.05       106.75       110.53       107.47 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        11.34        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
        7.96        10.42        25.32        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       19.86        12.03        12.49        16.60        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       10.65        22.29         4.47         4.73         4.21       303.09 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 
      127.56        29.16        19.59        32.88         5.98        17.46 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        26.14         7.69        12.20         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       21.44        46.22        12.99        24.82         1.61        11.74 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        9.47        71.05        56.52         1.35        92.78         6.90 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            27.62              0.10 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            98.07            303.09 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            72.79             14.35 
[1] "27.6 - 98.1 (72.8)" "0.1 - 303.1 (14.3)"
[1] "hr="     "2.6e+07"
D4V2, continuous
D4V3, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    1  2
  4P GAIN WILD-TYPE 72 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    2
  4P GAIN WILD-TYPE   72   54
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               1                72
  MALE                 2                54
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     1
  4P GAIN WILD-TYPE                                1     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           0     2
  4P GAIN WILD-TYPE                         9   110
D4V4, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                      0                 9
  WHITE                                          2               110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = 4Q GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     3   0
  4Q GAIN WILD-TYPE 122   4
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               126 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                0                 4 
$`4Q GAIN MUTATED`
TCGA-RW-A688 TCGA-SP-A6QI TCGA-WB-A80K 
        1.22        98.07        27.62 

$`4Q GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       19.86         2.93         7.10        33.30        23.80         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
        0.85        13.32        11.70        13.05         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02         0.69         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        0.59        20.09        24.00        26.30        23.51        14.50 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       11.38        29.88        29.98        19.76        17.33        10.65 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD 
       11.77         6.08         7.89        12.20       104.55       101.49 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       70.65        67.07         9.01        99.06         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
       51.22        54.44        73.05       106.75       110.53       107.47 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        11.34        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
        7.96        10.42        25.32        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       19.86        12.03        12.49        16.60        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       10.65        22.29         4.47         4.73         4.21       303.09 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 
      127.56        29.16        19.59        32.88         5.98        17.46 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        26.14         7.69        12.20         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       21.44        46.22        12.99        24.82         1.61        11.74 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        9.47        71.05        56.52         1.35        92.78         6.90 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             1.22              0.10 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            98.07            303.09 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            27.62             14.76 
[1] "1.2 - 98.1 (27.6)"  "0.1 - 303.1 (14.8)"
[1] "hr="     "2.5e+07"
D5V2, continuous
D5V3, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    1  2
  4Q GAIN WILD-TYPE 72 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    2
  4Q GAIN WILD-TYPE   72   54
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               1                72
  MALE                 2                54
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     0
  4Q GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           0     3
  4Q GAIN WILD-TYPE                         9   109
D5V4, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      0                 9
  WHITE                                          3               109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = 5P GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED     9   0
  5P GAIN WILD-TYPE 116   4
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                9               120 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                0                 4 
$`5P GAIN MUTATED`
TCGA-S7-A7WL TCGA-SR-A6MT TCGA-SR-A6N0 TCGA-W2-A7H5 TCGA-WB-A80K TCGA-WB-A815 
       20.09       106.75        49.61        14.20        27.62         5.98 
TCGA-WB-A81A TCGA-WB-A81T TCGA-WB-A821 
       12.20         9.47         1.35 

$`5P GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       19.86         2.93         7.10        33.30        23.80         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        0.85        13.32         1.22        11.70        13.05         7.96 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 
        6.28        72.79        15.02         0.69         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        2.89         0.59        24.00        26.30        23.51        14.50 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       11.38        29.88        29.98        19.76        17.33        10.65 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD 
       11.77         6.08         7.89        12.20       104.55       101.49 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       70.65        67.07        98.07         9.01        99.06         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV 
        0.10        51.22        54.44        73.05       110.53       107.47 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
        3.12        24.66        11.34         4.34        25.15         7.96 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC 
       10.42        25.32        17.16         1.18        19.86        12.03 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80L 
       12.49        16.60        17.69        25.61        10.65        22.29 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       303.09       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
       19.59        32.88        17.46        32.61        26.14         7.69 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
        0.79        37.18        24.00        24.23        42.54         1.12 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
        1.87        19.56        21.44        46.22        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 TCGA-XG-A823 
        1.61        11.74        71.05        56.52        92.78         6.90 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             1.35              0.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           106.75            303.09 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            14.20             15.81 
[1] "1.4 - 106.8 (14.2)" "0.1 - 303.1 (15.8)"
[1] "hr="     "7.4e+07"
D6V2, continuous
D6V3, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    6  3
  5P GAIN WILD-TYPE 67 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      6    3
  5P GAIN WILD-TYPE   67   53
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               6                67
  MALE                 3                53
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  0     0
  5P GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                           0     9
  5P GAIN WILD-TYPE                         9   103
D6V4, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      0                 9
  WHITE                                          9               103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = 5Q GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED     6   0
  5Q GAIN WILD-TYPE 119   4
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6               123 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                0                 4 
$`5Q GAIN MUTATED`
TCGA-SR-A6MT TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-W2-A7H5 TCGA-WB-A80K TCGA-WB-A821 
      106.75        11.34        49.61        14.20        27.62         1.35 

$`5Q GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       19.86         2.93         7.10        33.30        23.80         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        0.85        13.32         1.22        11.70        13.05         7.96 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 
        6.28        72.79        15.02         0.69         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89         0.59        20.09        24.00        26.30        23.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       14.50        11.38        29.88        29.98        19.76        17.33 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC 
       10.65        11.77         6.08         7.89        12.20       104.55 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      101.49        70.65        67.07        98.07         9.01        99.06 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU 
        1.41         0.10        51.22        54.44        73.05       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
      107.47         3.12        24.66         4.34        25.15         7.96 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC 
       10.42        25.32        17.16         1.18        19.86        12.03 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80L 
       12.49        16.60        17.69        25.61        10.65        22.29 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       303.09       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 
       19.59        32.88         5.98        17.46        32.61        26.14 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
        7.69        12.20         0.79        37.18        24.00        24.23 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54         1.12         1.87        19.56        21.44        46.22 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       12.99        24.82         1.61        11.74         9.47        71.05 
TCGA-WB-A81W TCGA-WB-A822 TCGA-XG-A823 
       56.52        92.78         6.90 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             1.35              0.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           106.75            303.09 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            20.91             15.02 
[1] "1.4 - 106.8 (20.9)" "0.1 - 303.1 (15.0)"
[1] "hr="     "2.6e+07"
D7V2, continuous
D7V3, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    5  1
  5Q GAIN WILD-TYPE 68 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      5    1
  5Q GAIN WILD-TYPE   68   55
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               5                68
  MALE                 1                55
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     0
  5Q GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           0     6
  5Q GAIN WILD-TYPE                         9   106
D7V4, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      0                 9
  WHITE                                          6               106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = 6P GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    10   0
  6P GAIN WILD-TYPE 115   4
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               10               119 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                0                 4 
$`6P GAIN MUTATED`
TCGA-P8-A5KD TCGA-PR-A5PG TCGA-RM-A68W TCGA-RW-A684 TCGA-S7-A7WN TCGA-S7-A7X1 
        2.27        81.70         0.92         1.05        26.30         7.89 
TCGA-W2-A7H5 TCGA-WB-A80L TCGA-WB-A819 TCGA-WB-A821 
       14.20        22.29         7.69         1.35 

$`6P GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PH 
       31.46        29.03         0.95         5.88         7.89        28.01 
TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
        1.25        36.23         6.94         1.81         0.72        25.18 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RT-A6Y9 
        2.30         4.41         0.79         0.95        38.73        97.22 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       41.06         8.09        86.89        19.86         2.93         7.10 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 
       33.30        23.80         0.85        13.32         1.22        11.70 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G 
       13.05         7.96         6.28        72.79        15.02         0.69 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89         0.59        20.09        24.00 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       23.51        14.50        11.38        29.88        29.98        19.76 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SP-A6QC 
       17.33        10.65        11.77         6.08        12.20       104.55 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      101.49        70.65        67.07        98.07         9.01        99.06 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT 
        1.41         0.10        51.22        54.44        73.05       106.75 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
      110.53       107.47         3.12        24.66        11.34        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 
        4.34        25.15         7.96        10.42        25.32        17.16 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF 
        1.18        19.86        12.03        12.49        16.60        17.69 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       25.61        10.65        27.62         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      303.09       127.56        29.16        19.59        32.88         5.98 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       17.46        32.61        26.14        12.20         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       21.44        46.22        12.99        24.82         1.61        11.74 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 TCGA-XG-A823 
        9.47        71.05        56.52        92.78         6.90 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.92              0.10 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            81.70            303.09 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             7.79             17.16 
[1] "0.9 - 81.7 (7.8)"   "0.1 - 303.1 (17.2)"
[1] "hr="     "2.6e+07"
D8V2, continuous
D8V3, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    7  3
  6P GAIN WILD-TYPE 66 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      7    3
  6P GAIN WILD-TYPE   66   53
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               7                66
  MALE                 3                53
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0     0
  6P GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           0    10
  6P GAIN WILD-TYPE                         9   102
D8V4, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      0                 9
  WHITE                                         10               102
[1] 4 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 = 6Q GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED     4   0
  6Q GAIN WILD-TYPE 121   4
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4               125 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                0                 4 
$`6Q GAIN MUTATED`
TCGA-S7-A7X1 TCGA-W2-A7H5 TCGA-WB-A80L TCGA-WB-A821 
        7.89        14.20        22.29         1.35 

$`6Q GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       19.86         2.93         7.10        33.30        23.80         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        0.85        13.32         1.22        11.70        13.05         7.96 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 
        6.28        72.79        15.02         0.69         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89         0.59        20.09        24.00        26.30        23.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       14.50        11.38        29.88        29.98        19.76        17.33 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD 
       10.65        11.77         6.08        12.20       104.55       101.49 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       70.65        67.07        98.07         9.01        99.06         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
        0.10        51.22        54.44        73.05       106.75       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      107.47         3.12        24.66        11.34        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA 
       25.15         7.96        10.42        25.32        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       19.86        12.03        12.49        16.60        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       10.65        27.62         4.47         4.73         4.21       303.09 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 
      127.56        29.16        19.59        32.88         5.98        17.46 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        26.14         7.69        12.20         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       21.44        46.22        12.99        24.82         1.61        11.74 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 TCGA-XG-A823 
        9.47        71.05        56.52        92.78         6.90 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             1.35              0.10 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            22.29            303.09 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           11.045            16.600 
[1] "1.4 - 22.3 (11.0)"  "0.1 - 303.1 (16.6)"
[1] "hr="     "9300000"
D9V2, continuous
D9V3, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    3  1
  6Q GAIN WILD-TYPE 70 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3    1
  6Q GAIN WILD-TYPE   70   55
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               3                70
  MALE                 1                55
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     0
  6Q GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           0     4
  6Q GAIN WILD-TYPE                         9   108
D9V4, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      0                 9
  WHITE                                          4               108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = 7P GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    22   0
  7P GAIN WILD-TYPE 103   4
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               22               107 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                0                 4 
$`7P GAIN MUTATED`
TCGA-P8-A6RX TCGA-PR-A5PG TCGA-QT-A5XM TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RT-A6YC 
        0.95        81.70         0.72         0.79         0.95         8.09 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A68G TCGA-S7-A7WL TCGA-S7-A7WW TCGA-S7-A7X1 
       23.80         1.05         0.69        20.09        10.65         7.89 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6N0 TCGA-W2-A7H7 TCGA-WB-A80L TCGA-WB-A80O 
      106.75       110.53        49.61        17.16        22.29         4.21 
TCGA-WB-A815 TCGA-WB-A81A TCGA-WB-A81N TCGA-WB-A821 
        5.98        12.20        46.22         1.35 

$`7P GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PH 
       31.46        29.03         2.27         5.88         7.89        28.01 
TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XN TCGA-QT-A5XO 
        1.25        36.23         6.94         1.81        25.18         2.30 
TCGA-QT-A5XP TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RW-A67V 
        4.41        38.73         0.92        97.22        41.06        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A685 TCGA-RW-A686 
       19.86         2.93         7.10        33.30         0.85        13.32 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D 
        1.22        11.70        13.05         7.96         6.28        72.79 
TCGA-RW-A68F TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WM 
       15.02         4.41         1.78         2.89         0.59        24.00 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       26.30        23.51        14.50        11.38        29.88        29.98 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SP-A6QC 
       19.76        17.33        11.77         6.08        12.20       104.55 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      101.49        70.65        67.07        98.07         9.01        99.06 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MV 
        1.41         0.10        51.22        54.44        73.05       107.47 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
        3.12        24.66        11.34         4.34        25.15         7.96 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC 
       10.42        25.32        14.20         1.18        19.86        12.03 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       12.49        16.60        17.69        25.61        10.65        27.62 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.47         4.73       303.09       127.56        29.16        19.59 
TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D 
       32.88        17.46        32.61        26.14         7.69         0.79 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        24.00        24.23        42.54         1.12         1.87 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       19.56        21.44        12.99        24.82         1.61        11.74 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 TCGA-XG-A823 
        9.47        71.05        56.52        92.78         6.90 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.69              0.10 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           110.53            303.09 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             9.37             17.33 
[1] "0.7 - 110.5 (9.4)"  "0.1 - 303.1 (17.3)"
[1] "hr="     "8.3e+07"
D10V2, continuous
D10V3, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   11 11
  7P GAIN WILD-TYPE 62 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     11   11
  7P GAIN WILD-TYPE   62   45
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              11                62
  MALE                11                45
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  0     0
  7P GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                           0    22
  7P GAIN WILD-TYPE                         9    90
D10V4, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      0                 9
  WHITE                                         22                90
[1] 4 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 = 7Q GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    18   0
  7Q GAIN WILD-TYPE 107   4
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               18               111 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                0                 4 
$`7Q GAIN MUTATED`
TCGA-P8-A6RX TCGA-QT-A5XM TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RT-A6YC TCGA-RW-A681 
        0.95         0.72         0.79         0.95         8.09        23.80 
TCGA-RW-A684 TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WW TCGA-S7-A7X1 TCGA-SR-A6MT 
        1.05         0.59        20.09        10.65         7.89       106.75 
TCGA-SR-A6MU TCGA-SR-A6N0 TCGA-W2-A7H7 TCGA-WB-A80L TCGA-WB-A81A TCGA-WB-A821 
      110.53        49.61        17.16        22.29        12.20         1.35 

$`7Q GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       31.46        29.03         2.27         5.88         7.89        81.70 
TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XN 
       28.01         1.25        36.23         6.94         1.81        25.18 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA 
        2.30         4.41        38.73         0.92        97.22        41.06 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A685 
       86.89        19.86         2.93         7.10        33.30         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
       13.32         1.22        11.70        13.05         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02         0.69         4.41         1.78         2.89 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       24.00        26.30        23.51        14.50        11.38        29.88 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 
       29.98        19.76        17.33        11.77         6.08        12.20 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      104.55       101.49        70.65        67.07        98.07         9.01 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
       99.06         1.41         0.10        51.22        54.44        73.05 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK 
      107.47         3.12        24.66        11.34         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HB 
        7.96        10.42        25.32        14.20         1.18        19.86 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY 
       12.03        12.49        16.60        17.69        25.61        10.65 
TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       27.62         4.47         4.73         4.21       303.09       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 
       29.16        19.59        32.88         5.98        17.46        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
       26.14         7.69         0.79        37.18        24.00        24.23 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54         1.12         1.87        19.56        21.44        46.22 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       12.99        24.82         1.61        11.74         9.47        71.05 
TCGA-WB-A81W TCGA-WB-A822 TCGA-XG-A823 
       56.52        92.78         6.90 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.59              0.10 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           110.53            303.09 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             9.37             17.33 
[1] "0.6 - 110.5 (9.4)"  "0.1 - 303.1 (17.3)"
[1] "hr="     "7.7e+07"
D11V2, continuous
D11V3, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    7 11
  7Q GAIN WILD-TYPE 66 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7   11
  7Q GAIN WILD-TYPE   66   45
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               7                66
  MALE                11                45
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  0     0
  7Q GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                           0    18
  7Q GAIN WILD-TYPE                         9    94
D11V4, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      0                 9
  WHITE                                         18                94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = 8P GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED     7   0
  8P GAIN WILD-TYPE 118   4
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7               122 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                0                 4 
$`8P GAIN MUTATED`
TCGA-QT-A5XN TCGA-RM-A68W TCGA-RW-A681 TCGA-S7-A7WW TCGA-SR-A6MS TCGA-SR-A6MU 
       25.18         0.92        23.80        10.65        73.05       110.53 
TCGA-SR-A6N0 
       49.61 

$`8P GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
        0.72         2.30         4.41         0.79         0.95        38.73 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
       97.22        41.06         8.09        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
        7.10        33.30         1.05         0.85        13.32         1.22 
TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F 
       11.70        13.05         7.96         6.28        72.79        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        0.69         4.41         1.78         2.89         0.59        20.09 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       24.00        26.30        23.51        14.50        11.38        29.88 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 
       29.98        19.76        17.33        11.77         6.08         7.89 
TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
       12.20       104.55       101.49        70.65        67.07        98.07 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
        9.01        99.06         1.41         0.10        51.22        54.44 
TCGA-SR-A6MT TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ 
      106.75       107.47         3.12        24.66        11.34         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       25.15         7.96        10.42        25.32        14.20        17.16 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF 
        1.18        19.86        12.03        12.49        16.60        17.69 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        10.65        27.62        22.29         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       303.09       127.56        29.16        19.59        32.88 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A 
        5.98        17.46        32.61        26.14         7.69        12.20 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
        0.79        37.18        24.00        24.23        42.54         1.12 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
        1.87        19.56        21.44        46.22        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 
        1.61        11.74         9.47        71.05        56.52         1.35 
TCGA-WB-A822 TCGA-XG-A823 
       92.78         6.90 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.92              0.10 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           110.53            303.09 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            25.18             14.35 
[1] "0.9 - 110.5 (25.2)" "0.1 - 303.1 (14.3)"
[1] "hr="     "7.4e+07"
D12V2, continuous
D12V3, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    5  2
  8P GAIN WILD-TYPE 68 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    2
  8P GAIN WILD-TYPE   68   54
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               5                68
  MALE                 2                54
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     0
  8P GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           1     6
  8P GAIN WILD-TYPE                         8   106
D12V4, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      1                 8
  WHITE                                          6               106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = 8Q GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED     9   1
  8Q GAIN WILD-TYPE 116   3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               10               119 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                1                 3 
$`8Q GAIN MUTATED`
TCGA-QT-A5XN TCGA-RM-A68W TCGA-RW-A681 TCGA-RW-A8AZ TCGA-S7-A7WW TCGA-SP-A6QF 
       25.18         0.92        23.80         2.89        10.65        70.65 
TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6N0 TCGA-W2-A7HE 
       73.05       110.53        49.61        16.60 

$`8Q GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
        0.72         2.30         4.41         0.79         0.95        38.73 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
       97.22        41.06         8.09        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
        7.10        33.30         1.05         0.85        13.32         1.22 
TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F 
       11.70        13.05         7.96         6.28        72.79        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        0.69         4.41         1.78         0.59        20.09        24.00 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       26.30        23.51        14.50        11.38        29.88        29.98 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       19.76        17.33        11.77         6.08         7.89        12.20 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      104.55       101.49        67.07        98.07         9.01        99.06 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MT TCGA-SR-A6MV 
        1.41         0.10        51.22        54.44       106.75       107.47 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
        3.12        24.66        11.34         4.34        25.15         7.96 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
       10.42        25.32        14.20        17.16         1.18        19.86 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       12.03        12.49        17.69        25.61        10.65        27.62 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       22.29         4.47         4.73         4.21       303.09       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 
       29.16        19.59        32.88         5.98        17.46        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       26.14         7.69        12.20         0.79        37.18        24.00 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       24.23        42.54         1.12         1.87        19.56        21.44 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       46.22        12.99        24.82         1.61        11.74         9.47 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        56.52         1.35        92.78         6.90 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.92              0.10 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           110.53            303.09 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            24.49             14.20 
[1] "0.9 - 110.5 (24.5)" "0.1 - 303.1 (14.2)"
[1] "hr=" "3.2"
D13V2, continuous
D13V3, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    5  5
  8Q GAIN WILD-TYPE 68 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5    5
  8Q GAIN WILD-TYPE   68   51
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               5                68
  MALE                 5                51
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     1
  8Q GAIN WILD-TYPE                                1     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                           1     8
  8Q GAIN WILD-TYPE                         8   104
D13V4, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                      1                 8
  WHITE                                          8               104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = 9P GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     3   0
  9P GAIN WILD-TYPE 122   4
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               126 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                 4 
$`9P GAIN MUTATED`
TCGA-SR-A6MT TCGA-W2-A7H7 TCGA-WB-A80L 
      106.75        17.16        22.29 

$`9P GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       19.86         2.93         7.10        33.30        23.80         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        0.85        13.32         1.22        11.70        13.05         7.96 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 
        6.28        72.79        15.02         0.69         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89         0.59        20.09        24.00        26.30        23.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       14.50        11.38        29.88        29.98        19.76        17.33 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC 
       10.65        11.77         6.08         7.89        12.20       104.55 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      101.49        70.65        67.07        98.07         9.01        99.06 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU 
        1.41         0.10        51.22        54.44        73.05       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      107.47         3.12        24.66        11.34        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HA 
       25.15         7.96        10.42        25.32        14.20         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       19.86        12.03        12.49        16.60        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       10.65        27.62         4.47         4.73         4.21       303.09 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 
      127.56        29.16        19.59        32.88         5.98        17.46 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        26.14         7.69        12.20         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       21.44        46.22        12.99        24.82         1.61        11.74 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        9.47        71.05        56.52         1.35        92.78         6.90 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            17.16              0.10 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           106.75            303.09 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            22.29             14.35 
[1] "17.2 - 106.8 (22.3)" "0.1 - 303.1 (14.3)" 
[1] "hr="     "2.5e+07"
D14V2, continuous
D14V3, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    2  1
  9P GAIN WILD-TYPE 71 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    1
  9P GAIN WILD-TYPE   71   55
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               2                71
  MALE                 1                55
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     0
  9P GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           0     3
  9P GAIN WILD-TYPE                         9   109
D14V4, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      0                 9
  WHITE                                          3               109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = 10P GAIN MUTATION ANALYSIS
D15V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     9   0
  10P GAIN WILD-TYPE 116   4
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 9                120 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 0                  4 
$`10P GAIN MUTATED`
TCGA-RW-A681 TCGA-RW-A688 TCGA-RW-A68B TCGA-SR-A6MT TCGA-SR-A6MZ TCGA-W2-A7H5 
       23.80         1.22         7.96       106.75        11.34        14.20 
TCGA-W2-A7HE TCGA-WB-A80L TCGA-WB-A81A 
       16.60        22.29        12.20 

$`10P GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 
       19.86         2.93         7.10        33.30         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F 
       13.32        11.70        13.05         6.28        72.79        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        0.69         4.41         1.78         2.89         0.59        20.09 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       24.00        26.30        23.51        14.50        11.38        29.88 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       29.98        19.76        17.33        10.65        11.77         6.08 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
        7.89        12.20       104.55       101.49        70.65        67.07 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
       98.07         9.01        99.06         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY 
       54.44        73.05       110.53       107.47         3.12        24.66 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15         7.96        10.42        25.32 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HF 
       17.16         1.18        19.86        12.03        12.49        17.69 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       25.61        10.65        27.62         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      303.09       127.56        29.16        19.59        32.88         5.98 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81E 
       17.46        32.61        26.14         7.69         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       21.44        46.22        12.99        24.82         1.61        11.74 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        9.47        71.05        56.52         1.35        92.78         6.90 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1.22               0.10 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            106.75             303.09 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             14.20              16.09 
[1] "1.2 - 106.8 (14.2)" "0.1 - 303.1 (16.1)"
[1] "hr="     "2.7e+07"
D15V2, continuous
D15V3, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    6  3
  10P GAIN WILD-TYPE 67 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      6    3
  10P GAIN WILD-TYPE   67   53
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                6                 67
  MALE                  3                 53
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0     0
  10P GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           0     8
  10P GAIN WILD-TYPE                         9   104
D15V4, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                           8                104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = 10Q GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     8   0
  10Q GAIN WILD-TYPE 117   4
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                121 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 0                  4 
$`10Q GAIN MUTATED`
TCGA-RW-A681 TCGA-RW-A688 TCGA-RW-A68B TCGA-SP-A6QC TCGA-SR-A6MT TCGA-SR-A6MZ 
       23.80         1.22         7.96       104.55       106.75        11.34 
TCGA-W2-A7H5 TCGA-W2-A7HE 
       14.20        16.60 

$`10Q GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 
       19.86         2.93         7.10        33.30         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F 
       13.32        11.70        13.05         6.28        72.79        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        0.69         4.41         1.78         2.89         0.59        20.09 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       24.00        26.30        23.51        14.50        11.38        29.88 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       29.98        19.76        17.33        10.65        11.77         6.08 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
        7.89        12.20       101.49        70.65        67.07        98.07 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
        9.01        99.06         1.41         0.10        51.22        54.44 
TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6N0 
       73.05       110.53       107.47         3.12        24.66        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 
        4.34        25.15         7.96        10.42        25.32        17.16 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HF TCGA-W2-A7HH 
        1.18        19.86        12.03        12.49        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       10.65        27.62        22.29         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      303.09       127.56        29.16        19.59        32.88         5.98 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
       17.46        32.61        26.14         7.69        12.20         0.79 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        24.00        24.23        42.54         1.12         1.87 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       19.56        21.44        46.22        12.99        24.82         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       11.74         9.47        71.05        56.52         1.35        92.78 
TCGA-XG-A823 
        6.90 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1.22               0.10 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            106.75             303.09 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             15.40              15.02 
[1] "1.2 - 106.8 (15.4)" "0.1 - 303.1 (15.0)"
[1] "hr="     "2.7e+07"
D16V2, continuous
D16V3, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    4  4
  10Q GAIN WILD-TYPE 69 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      4    4
  10Q GAIN WILD-TYPE   69   52
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                4                 69
  MALE                  4                 52
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     0
  10Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           0     7
  10Q GAIN WILD-TYPE                         9   105
D16V4, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                           7                105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = 11P GAIN MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     5   0
  11P GAIN WILD-TYPE 120   4
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                124 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                  4 
$`11P GAIN MUTATED`
TCGA-P8-A5KD TCGA-PR-A5PF TCGA-RW-A689 TCGA-W2-A7H5 TCGA-WB-A80O 
        2.27         7.89        11.70        14.20         4.21 

$`11P GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG TCGA-PR-A5PH 
       31.46        29.03         0.95         5.88        81.70        28.01 
TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
        1.25        36.23         6.94         1.81         0.72        25.18 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        2.30         4.41         0.79         0.95        38.73         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
       97.22        41.06         8.09        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        7.10        33.30        23.80         1.05         0.85        13.32 
TCGA-RW-A688 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F 
        1.22        13.05         7.96         6.28        72.79        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        0.69         4.41         1.78         2.89         0.59        20.09 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       24.00        26.30        23.51        14.50        11.38        29.88 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       29.98        19.76        17.33        10.65        11.77         6.08 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
        7.89        12.20       104.55       101.49        70.65        67.07 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
       98.07         9.01        99.06         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX 
       54.44        73.05       106.75       110.53       107.47         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        11.34        49.61         4.34        25.15         7.96 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC 
       10.42        25.32        17.16         1.18        19.86        12.03 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       12.49        16.60        17.69        25.61        10.65        27.62 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
       22.29         4.47         4.73       303.09       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 
       19.59        32.88         5.98        17.46        32.61        26.14 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
        7.69        12.20         0.79        37.18        24.00        24.23 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54         1.12         1.87        19.56        21.44        46.22 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       12.99        24.82         1.61        11.74         9.47        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       56.52         1.35        92.78         6.90 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              2.27               0.10 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             14.20             303.09 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             7.890             17.245 
[1] "2.3 - 14.2 (7.9)"   "0.1 - 303.1 (17.2)"
[1] "hr="     "9500000"
D17V2, continuous
D17V3, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    4  1
  11P GAIN WILD-TYPE 69 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      4    1
  11P GAIN WILD-TYPE   69   55
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                4                 69
  MALE                  1                 55
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     0
  11P GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           0     5
  11P GAIN WILD-TYPE                         9   107
D17V4, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                           5                107
[1] 4 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 = 12P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED     7   0
  12P GAIN WILD-TYPE 118   4
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                122 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 0                  4 
$`12P GAIN MUTATED`
TCGA-RW-A681 TCGA-S7-A7X1 TCGA-SR-A6MP TCGA-SR-A6MT TCGA-SR-A6MZ TCGA-W2-A7H5 
       23.80         7.89        51.22       106.75        11.34        14.20 
TCGA-WB-A821 
        1.35 

$`12P GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 
       19.86         2.93         7.10        33.30         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
       13.32         1.22        11.70        13.05         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02         0.69         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        0.59        20.09        24.00        26.30        23.51        14.50 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       11.38        29.88        29.98        19.76        17.33        10.65 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       11.77         6.08        12.20       104.55       101.49        70.65 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.07        98.07         9.01        99.06         1.41         0.10 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY 
       54.44        73.05       110.53       107.47         3.12        24.66 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15         7.96        10.42        25.32 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       17.16         1.18        19.86        12.03        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       17.69        25.61        10.65        27.62        22.29         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       303.09       127.56        29.16        19.59 
TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
       32.88         5.98        17.46        32.61        26.14         7.69 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       12.20         0.79        37.18        24.00        24.23        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
        1.12         1.87        19.56        21.44        46.22        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        11.74         9.47        71.05        56.52 
TCGA-WB-A822 TCGA-XG-A823 
       92.78         6.90 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.35               0.10 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            106.75             303.09 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             14.20              15.81 
[1] "1.4 - 106.8 (14.2)" "0.1 - 303.1 (15.8)"
[1] "hr="     "2.6e+07"
D18V2, continuous
D18V3, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    5  2
  12P GAIN WILD-TYPE 68 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      5    2
  12P GAIN WILD-TYPE   68   54
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                5                 68
  MALE                  2                 54
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     0
  12P GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                           0     7
  12P GAIN WILD-TYPE                         9   105
D18V4, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                           7                105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = 12Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    10   0
  12Q GAIN WILD-TYPE 115   4
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                10                119 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                  4 
$`12Q GAIN MUTATED`
TCGA-PR-A5PF TCGA-RW-A681 TCGA-S7-A7WN TCGA-S7-A7X1 TCGA-SR-A6MP TCGA-SR-A6MT 
        7.89        23.80        26.30         7.89        51.22       106.75 
TCGA-SR-A6MZ TCGA-W2-A7H5 TCGA-W2-A7HD TCGA-WB-A821 
       11.34        14.20        12.49         1.35 

$`12Q GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG 
       31.46        29.03         2.27         0.95         5.88        81.70 
TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       28.01         1.25        36.23         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
       25.18         2.30         4.41         0.79         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92        97.22        41.06         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        2.93         7.10        33.30         1.05         0.85        13.32 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D 
        1.22        11.70        13.05         7.96         6.28        72.79 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       15.02         0.69         4.41         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       20.09        24.00        23.51        14.50        11.38        29.88 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       29.98        19.76        17.33        10.65        11.77         6.08 
TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
       12.20       104.55       101.49        70.65        67.07        98.07 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MS 
        9.01        99.06         1.41         0.10        54.44        73.05 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6N0 TCGA-TT-A6YJ 
      110.53       107.47         3.12        24.66        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA 
       25.15         7.96        10.42        25.32        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY 
       19.86        12.03        16.60        17.69        25.61        10.65 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       27.62        22.29         4.47         4.73         4.21       303.09 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 
      127.56        29.16        19.59        32.88         5.98        17.46 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        26.14         7.69        12.20         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       21.44        46.22        12.99        24.82         1.61        11.74 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 TCGA-XG-A823 
        9.47        71.05        56.52        92.78         6.90 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.35               0.10 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            106.75             303.09 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            13.345             16.600 
[1] "1.4 - 106.8 (13.3)" "0.1 - 303.1 (16.6)"
[1] "hr="     "7.5e+07"
D19V2, continuous
D19V3, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    7  3
  12Q GAIN WILD-TYPE 66 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      7    3
  12Q GAIN WILD-TYPE   66   53
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                7                 66
  MALE                  3                 53
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     0
  12Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                           0    10
  12Q GAIN WILD-TYPE                         9   102
D19V4, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                          10                102
[1] 4 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 = 13Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED     7   0
  13Q GAIN WILD-TYPE 118   4
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 7                122 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 0                  4 
$`13Q GAIN MUTATED`
TCGA-P8-A6RX TCGA-QT-A69Q TCGA-RW-A68F TCGA-S7-A7X1 TCGA-SR-A6MT TCGA-SR-A6N0 
        0.95         0.79        15.02         7.89       106.75        49.61 
TCGA-WB-A821 
        1.35 

$`13Q GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       31.46        29.03         2.27         5.88         7.89        81.70 
TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       28.01         1.25        36.23         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
       25.18         2.30         4.41         0.95        38.73         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
       97.22        41.06         8.09        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        7.10        33.30        23.80         1.05         0.85        13.32 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D 
        1.22        11.70        13.05         7.96         6.28        72.79 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        0.69         4.41         1.78         2.89         0.59        20.09 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       24.00        26.30        23.51        14.50        11.38        29.88 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       29.98        19.76        17.33        10.65        11.77         6.08 
TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
       12.20       104.55       101.49        70.65        67.07        98.07 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
        9.01        99.06         1.41         0.10        51.22        54.44 
TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
       73.05       110.53       107.47         3.12        24.66        11.34 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        25.15         7.96        10.42        25.32        14.20 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       17.16         1.18        19.86        12.03        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       17.69        25.61        10.65        27.62        22.29         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       303.09       127.56        29.16        19.59 
TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
       32.88         5.98        17.46        32.61        26.14         7.69 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       12.20         0.79        37.18        24.00        24.23        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
        1.12         1.87        19.56        21.44        46.22        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        11.74         9.47        71.05        56.52 
TCGA-WB-A822 TCGA-XG-A823 
       92.78         6.90 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.79               0.10 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            106.75             303.09 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              7.89              16.88 
[1] "0.8 - 106.8 (7.9)"  "0.1 - 303.1 (16.9)"
[1] "hr="     "2.6e+07"
D20V2, continuous
D20V3, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    4  3
  13Q GAIN WILD-TYPE 69 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    3
  13Q GAIN WILD-TYPE   69   53
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                4                 69
  MALE                  3                 53
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     0
  13Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           0     7
  13Q GAIN WILD-TYPE                         9   105
D20V4, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                           7                105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = 15Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    10   0
  15Q GAIN WILD-TYPE 115   4
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                119 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 0                  4 
$`15Q GAIN MUTATED`
TCGA-RW-A681 TCGA-S7-A7WN TCGA-S7-A7WW TCGA-S7-A7X1 TCGA-SP-A6QF TCGA-W2-A7H5 
       23.80        26.30        10.65         7.89        70.65        14.20 
TCGA-W2-A7UY TCGA-WB-A80L TCGA-WB-A81A TCGA-WB-A81D 
       10.65        22.29        12.20         0.79 

$`15Q GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 
       19.86         2.93         7.10        33.30         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
       13.32         1.22        11.70        13.05         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02         0.69         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
        0.59        20.09        24.00        23.51        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X0 
       29.88        29.98        19.76        17.33        11.77         6.08 
TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
       12.20       104.55       101.49        67.07        98.07         9.01 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
       99.06         1.41         0.10        51.22        54.44        73.05 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
      106.75       110.53       107.47         3.12        24.66        11.34 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15         7.96        10.42        25.32 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       17.16         1.18        19.86        12.03        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       17.69        25.61        27.62         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      303.09       127.56        29.16        19.59        32.88         5.98 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81E TCGA-WB-A81F 
       17.46        32.61        26.14         7.69        37.18        24.00 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       24.23        42.54         1.12         1.87        19.56        21.44 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       46.22        12.99        24.82         1.61        11.74         9.47 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        56.52         1.35        92.78         6.90 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.79               0.10 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             70.65             303.09 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              13.2               16.6 
[1] "0.8 - 70.7 (13.2)"  "0.1 - 303.1 (16.6)"
[1] "hr="     "7.4e+07"
D21V2, continuous
D21V3, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    5  5
  15Q GAIN WILD-TYPE 68 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      5    5
  15Q GAIN WILD-TYPE   68   51
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                5                 68
  MALE                  5                 51
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     1
  15Q GAIN WILD-TYPE                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           0     9
  15Q GAIN WILD-TYPE                         9   103
D21V4, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                           9                103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = 16P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED     5   0
  16P GAIN WILD-TYPE 120   4
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                124 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 0                  4 
$`16P GAIN MUTATED`
TCGA-RW-A681 TCGA-RX-A8JQ TCGA-SR-A6MP TCGA-W2-A7H5 TCGA-WB-A81A 
       23.80         0.59        51.22        14.20        12.20 

$`16P GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 
       19.86         2.93         7.10        33.30         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
       13.32         1.22        11.70        13.05         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02         0.69         4.41         1.78         2.89 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       20.09        24.00        26.30        23.51        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       29.88        29.98        19.76        17.33        10.65        11.77 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
        6.08         7.89        12.20       104.55       101.49        70.65 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.07        98.07         9.01        99.06         1.41         0.10 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX 
       54.44        73.05       106.75       110.53       107.47         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        11.34        49.61         4.34        25.15         7.96 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC 
       10.42        25.32        17.16         1.18        19.86        12.03 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       12.49        16.60        17.69        25.61        10.65        27.62 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       22.29         4.47         4.73         4.21       303.09       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 
       29.16        19.59        32.88         5.98        17.46        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
       26.14         7.69         0.79        37.18        24.00        24.23 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54         1.12         1.87        19.56        21.44        46.22 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       12.99        24.82         1.61        11.74         9.47        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       56.52         1.35        92.78         6.90 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.59               0.10 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             51.22             303.09 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             14.20              15.81 
[1] "0.6 - 51.2 (14.2)"  "0.1 - 303.1 (15.8)"
[1] "hr="     "2.6e+07"
D22V2, continuous
D22V3, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    3  2
  16P GAIN WILD-TYPE 70 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3    2
  16P GAIN WILD-TYPE   70   54
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                3                 70
  MALE                  2                 54
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  0     0
  16P GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                           0     5
  16P GAIN WILD-TYPE                         9   107
D22V4, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                           5                107
[1] 4 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 = 16Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED     4   0
  16Q GAIN WILD-TYPE 121   4
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 4                125 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 0                  4 
$`16Q GAIN MUTATED`
TCGA-RW-A681 TCGA-RX-A8JQ TCGA-SR-A6MP TCGA-W2-A7H5 
       23.80         0.59        51.22        14.20 

$`16Q GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 
       19.86         2.93         7.10        33.30         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
       13.32         1.22        11.70        13.05         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02         0.69         4.41         1.78         2.89 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       20.09        24.00        26.30        23.51        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       29.88        29.98        19.76        17.33        10.65        11.77 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
        6.08         7.89        12.20       104.55       101.49        70.65 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.07        98.07         9.01        99.06         1.41         0.10 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX 
       54.44        73.05       106.75       110.53       107.47         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        11.34        49.61         4.34        25.15         7.96 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC 
       10.42        25.32        17.16         1.18        19.86        12.03 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       12.49        16.60        17.69        25.61        10.65        27.62 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       22.29         4.47         4.73         4.21       303.09       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 
       29.16        19.59        32.88         5.98        17.46        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       26.14         7.69        12.20         0.79        37.18        24.00 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       24.23        42.54         1.12         1.87        19.56        21.44 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       46.22        12.99        24.82         1.61        11.74         9.47 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        56.52         1.35        92.78         6.90 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.59               0.10 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             51.22             303.09 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             19.00              15.02 
[1] "0.6 - 51.2 (19.0)"  "0.1 - 303.1 (15.0)"
[1] "hr="     "2.5e+07"
D23V2, continuous
D23V3, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    2  2
  16Q GAIN WILD-TYPE 71 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2    2
  16Q GAIN WILD-TYPE   71   54
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                2                 71
  MALE                  2                 54
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  0     0
  16Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                           0     4
  16Q GAIN WILD-TYPE                         9   108
D23V4, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                           4                108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = 17Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED     4   0
  17Q GAIN WILD-TYPE 121   4
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 4                125 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 0                  4 
$`17Q GAIN MUTATED`
TCGA-QT-A5XP TCGA-RW-A681 TCGA-WB-A81J TCGA-WB-A81W 
        4.41        23.80         1.87        56.52 

$`17Q GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
        0.72        25.18         2.30         0.79         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92        97.22        41.06         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        2.93         7.10        33.30         1.05         0.85        13.32 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D 
        1.22        11.70        13.05         7.96         6.28        72.79 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       15.02         0.69         4.41         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       20.09        24.00        26.30        23.51        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       29.88        29.98        19.76        17.33        10.65        11.77 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
        6.08         7.89        12.20       104.55       101.49        70.65 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.07        98.07         9.01        99.06         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
       51.22        54.44        73.05       106.75       110.53       107.47 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        11.34        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
        7.96        10.42        25.32        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       19.86        12.03        12.49        16.60        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       10.65        27.62        22.29         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      303.09       127.56        29.16        19.59        32.88         5.98 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
       17.46        32.61        26.14         7.69        12.20         0.79 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81K 
       37.18        24.00        24.23        42.54         1.12        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       21.44        46.22        12.99        24.82         1.61        11.74 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        9.47        71.05         1.35        92.78         6.90 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              1.87               0.10 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             56.52             303.09 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            14.105             15.020 
[1] "1.9 - 56.5 (14.1)"  "0.1 - 303.1 (15.0)"
[1] "hr="     "2.5e+07"
D24V2, continuous
D24V3, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    1  3
  17Q GAIN WILD-TYPE 72 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1    3
  17Q GAIN WILD-TYPE   72   53
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                1                 72
  MALE                  3                 53
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0     0
  17Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                           1     3
  17Q GAIN WILD-TYPE                         8   109
D24V4, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       1                  8
  WHITE                                           3                109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = 18P GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED     4   0
  18P GAIN WILD-TYPE 121   4
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                125 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                  4 
$`18P GAIN MUTATED`
TCGA-RT-A6YA TCGA-RW-A681 TCGA-SR-A6MT TCGA-WB-A80L 
       41.06        23.80       106.75        22.29 

$`18P GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
       38.73         0.92        97.22         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        2.93         7.10        33.30         1.05         0.85        13.32 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D 
        1.22        11.70        13.05         7.96         6.28        72.79 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       15.02         0.69         4.41         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       20.09        24.00        26.30        23.51        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       29.88        29.98        19.76        17.33        10.65        11.77 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
        6.08         7.89        12.20       104.55       101.49        70.65 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.07        98.07         9.01        99.06         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX 
       51.22        54.44        73.05       110.53       107.47         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        11.34        49.61         4.34        25.15         7.96 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
       10.42        25.32        14.20        17.16         1.18        19.86 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY 
       12.03        12.49        16.60        17.69        25.61        10.65 
TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       27.62         4.47         4.73         4.21       303.09       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 
       29.16        19.59        32.88         5.98        17.46        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       26.14         7.69        12.20         0.79        37.18        24.00 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       24.23        42.54         1.12         1.87        19.56        21.44 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       46.22        12.99        24.82         1.61        11.74         9.47 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        56.52         1.35        92.78         6.90 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             22.29               0.10 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            106.75             303.09 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             32.43              14.20 
[1] "22.3 - 106.8 (32.4)" "0.1 - 303.1 (14.2)" 
[1] "hr="     "2.6e+07"
D25V2, continuous
D25V3, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    3  1
  18P GAIN WILD-TYPE 70 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3    1
  18P GAIN WILD-TYPE   70   55
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                3                 70
  MALE                  1                 55
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     0
  18P GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           0     4
  18P GAIN WILD-TYPE                         9   108
D25V4, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                           4                108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = 18Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED     7   0
  18Q GAIN WILD-TYPE 118   4
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 7                122 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                  4 
$`18Q GAIN MUTATED`
TCGA-P8-A5KD TCGA-RT-A6YA TCGA-RW-A681 TCGA-SR-A6MS TCGA-SR-A6MT TCGA-WB-A80L 
        2.27        41.06        23.80        73.05       106.75        22.29 
TCGA-WB-A81W 
       56.52 

$`18Q GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       31.46        29.03         0.95         5.88         7.89        81.70 
TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       28.01         1.25        36.23         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
       25.18         2.30         4.41         0.79         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
        0.92        97.22         8.09        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
        7.10        33.30         1.05         0.85        13.32         1.22 
TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F 
       11.70        13.05         7.96         6.28        72.79        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        0.69         4.41         1.78         2.89         0.59        20.09 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       24.00        26.30        23.51        14.50        11.38        29.88 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       29.98        19.76        17.33        10.65        11.77         6.08 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
        7.89        12.20       104.55       101.49        70.65        67.07 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
       98.07         9.01        99.06         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
       54.44       110.53       107.47         3.12        24.66        11.34 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15         7.96        10.42        25.32 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD 
       14.20        17.16         1.18        19.86        12.03        12.49 
TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M 
       16.60        17.69        25.61        10.65        27.62         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       303.09       127.56        29.16        19.59 
TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
       32.88         5.98        17.46        32.61        26.14         7.69 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       12.20         0.79        37.18        24.00        24.23        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
        1.12         1.87        19.56        21.44        46.22        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A821 
       24.82         1.61        11.74         9.47        71.05         1.35 
TCGA-WB-A822 TCGA-XG-A823 
       92.78         6.90 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              2.27               0.10 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            106.75             303.09 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             41.06              13.76 
[1] "2.3 - 106.8 (41.1)" "0.1 - 303.1 (13.8)"
[1] "hr="     "7.5e+07"
D26V2, continuous
D26V3, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    5  2
  18Q GAIN WILD-TYPE 68 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    2
  18Q GAIN WILD-TYPE   68   54
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                5                 68
  MALE                  2                 54
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     0
  18Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           0     7
  18Q GAIN WILD-TYPE                         9   105
D26V4, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                           7                105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = 19P GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    15   1
  19P GAIN WILD-TYPE 110   3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                16                113 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 1                  3 
$`19P GAIN MUTATED`
TCGA-RT-A6YA TCGA-RW-A681 TCGA-S7-A7WP TCGA-S7-A7WW TCGA-SQ-A6I6 TCGA-SR-A6MS 
       41.06        23.80        14.50        10.65         0.10        73.05 
TCGA-SR-A6MT TCGA-SR-A6N0 TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-WB-A80L TCGA-WB-A818 
      106.75        49.61        25.32        14.20        22.29        26.14 
TCGA-WB-A81A TCGA-WB-A81H TCGA-WB-A81Q TCGA-WB-A81S 
       12.20        42.54        24.82        11.74 

$`19P GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
       38.73         0.92        97.22         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        2.93         7.10        33.30         1.05         0.85        13.32 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D 
        1.22        11.70        13.05         7.96         6.28        72.79 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       15.02         0.69         4.41         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WQ TCGA-S7-A7WR 
       20.09        24.00        26.30        23.51        11.38        29.88 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 
       29.98        19.76        17.33        11.77         6.08         7.89 
TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
       12.20       104.55       101.49        70.65        67.07        98.07 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MU 
        9.01        99.06         1.41        51.22        54.44       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK 
      107.47         3.12        24.66        11.34         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC 
        7.96        10.42        17.16         1.18        19.86        12.03 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       12.49        16.60        17.69        25.61        10.65        27.62 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       303.09       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A819 
       19.59        32.88         5.98        17.46        32.61         7.69 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81I TCGA-WB-A81J 
        0.79        37.18        24.00        24.23         1.12         1.87 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81T 
       19.56        21.44        46.22        12.99         1.61         9.47 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        56.52         1.35        92.78         6.90 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.10               0.59 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            106.75             303.09 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             24.31              13.05 
[1] "0.1 - 106.8 (24.3)" "0.6 - 303.1 (13.1)"
[1] "hr=" "1.8"
D27V2, continuous
D27V3, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   11  5
  19P GAIN WILD-TYPE 62 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     11    5
  19P GAIN WILD-TYPE   62   51
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               11                 62
  MALE                  5                 51
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     0
  19P GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           0    16
  19P GAIN WILD-TYPE                         9    96
D27V4, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                          16                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = 19Q GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    11   0
  19Q GAIN WILD-TYPE 114   4
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                11                118 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                  4 
$`19Q GAIN MUTATED`
TCGA-RW-A681 TCGA-S7-A7WW TCGA-SQ-A6I6 TCGA-SR-A6MT TCGA-SR-A6N0 TCGA-TT-A6YP 
       23.80        10.65         0.10       106.75        49.61        25.32 
TCGA-W2-A7H5 TCGA-WB-A80L TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81H 
       14.20        22.29        26.14        12.20        42.54 

$`19Q GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 
       19.86         2.93         7.10        33.30         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
       13.32         1.22        11.70        13.05         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02         0.69         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        0.59        20.09        24.00        26.30        23.51        14.50 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WX 
       11.38        29.88        29.98        19.76        17.33        11.77 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
        6.08         7.89        12.20       104.55       101.49        70.65 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP 
       67.07        98.07         9.01        99.06         1.41        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY 
       54.44        73.05       110.53       107.47         3.12        24.66 
TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7H7 
       11.34         4.34        25.15         7.96        10.42        17.16 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF 
        1.18        19.86        12.03        12.49        16.60        17.69 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       25.61        10.65        27.62         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      303.09       127.56        29.16        19.59        32.88         5.98 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       17.46        32.61         7.69         0.79        37.18        24.00 
TCGA-WB-A81G TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       24.23         1.12         1.87        19.56        21.44        46.22 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       12.99        24.82         1.61        11.74         9.47        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       56.52         1.35        92.78         6.90 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.10               0.59 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            106.75             303.09 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             23.80              13.91 
[1] "0.1 - 106.8 (23.8)" "0.6 - 303.1 (13.9)"
[1] "hr="     "7.9e+07"
D28V2, continuous
D28V3, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    7  4
  19Q GAIN WILD-TYPE 66 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      7    4
  19Q GAIN WILD-TYPE   66   52
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                7                 66
  MALE                  4                 52
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     0
  19Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           0    11
  19Q GAIN WILD-TYPE                         9   101
D28V4, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                          11                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = 20P GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    10   0
  20P GAIN WILD-TYPE 115   4
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                10                119 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 0                  4 
$`20P GAIN MUTATED`
TCGA-PR-A5PF TCGA-RM-A68W TCGA-RW-A681 TCGA-SP-A6QI TCGA-SR-A6MT TCGA-TT-A6YN 
        7.89         0.92        23.80        98.07       106.75         7.96 
TCGA-WB-A80L TCGA-WB-A80N TCGA-WB-A81A TCGA-WB-A821 
       22.29         4.73        12.20         1.35 

$`20P GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG 
       31.46        29.03         2.27         0.95         5.88        81.70 
TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       28.01         1.25        36.23         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
       25.18         2.30         4.41         0.79         0.95        38.73 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
       97.22        41.06         8.09        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
        7.10        33.30         1.05         0.85        13.32         1.22 
TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F 
       11.70        13.05         7.96         6.28        72.79        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        0.69         4.41         1.78         2.89         0.59        20.09 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       24.00        26.30        23.51        14.50        11.38        29.88 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       29.98        19.76        17.33        10.65        11.77         6.08 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
        7.89        12.20       104.55       101.49        70.65        67.07 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
        9.01        99.06         1.41         0.10        51.22        54.44 
TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
       73.05       110.53       107.47         3.12        24.66        11.34 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
       49.61         4.34        25.15        10.42        25.32        14.20 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       17.16         1.18        19.86        12.03        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80O 
       17.69        25.61        10.65        27.62         4.47         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      303.09       127.56        29.16        19.59        32.88         5.98 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81E 
       17.46        32.61        26.14         7.69         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       21.44        46.22        12.99        24.82         1.61        11.74 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 TCGA-XG-A823 
        9.47        71.05        56.52        92.78         6.90 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.92               0.10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            106.75             303.09 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             10.08              16.60 
[1] "0.9 - 106.8 (10.1)" "0.1 - 303.1 (16.6)"
[1] "hr="     "7.4e+07"
D29V2, continuous
D29V3, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    7  3
  20P GAIN WILD-TYPE 66 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7    3
  20P GAIN WILD-TYPE   66   53
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                7                 66
  MALE                  3                 53
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0     0
  20P GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                           0    10
  20P GAIN WILD-TYPE                         9   102
D29V4, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                          10                102
[1] 4 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 = 20Q GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED     7   0
  20Q GAIN WILD-TYPE 118   4
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 7                122 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 0                  4 
$`20Q GAIN MUTATED`
TCGA-PR-A5PF TCGA-RW-A681 TCGA-SP-A6QI TCGA-SR-A6MT TCGA-WB-A80L TCGA-WB-A81A 
        7.89        23.80        98.07       106.75        22.29        12.20 
TCGA-WB-A821 
        1.35 

$`20Q GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG 
       31.46        29.03         2.27         0.95         5.88        81.70 
TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       28.01         1.25        36.23         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
       25.18         2.30         4.41         0.79         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92        97.22        41.06         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        2.93         7.10        33.30         1.05         0.85        13.32 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D 
        1.22        11.70        13.05         7.96         6.28        72.79 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       15.02         0.69         4.41         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       20.09        24.00        26.30        23.51        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       29.88        29.98        19.76        17.33        10.65        11.77 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
        6.08         7.89        12.20       104.55       101.49        70.65 
TCGA-SP-A6QG TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
       67.07         9.01        99.06         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY 
       54.44        73.05       110.53       107.47         3.12        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       11.34        49.61         4.34        25.15         7.96        10.42 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC 
       25.32        14.20        17.16         1.18        19.86        12.03 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       12.49        16.60        17.69        25.61        10.65        27.62 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       303.09       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 
       19.59        32.88         5.98        17.46        32.61        26.14 
TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
        7.69         0.79        37.18        24.00        24.23        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
        1.12         1.87        19.56        21.44        46.22        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        11.74         9.47        71.05        56.52 
TCGA-WB-A822 TCGA-XG-A823 
       92.78         6.90 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              1.35               0.10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            106.75             303.09 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             22.29              14.76 
[1] "1.4 - 106.8 (22.3)" "0.1 - 303.1 (14.8)"
[1] "hr="     "2.7e+07"
D30V2, continuous
D30V3, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    5  2
  20Q GAIN WILD-TYPE 68 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5    2
  20Q GAIN WILD-TYPE   68   54
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                5                 68
  MALE                  2                 54
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0     0
  20Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                           0     7
  20Q GAIN WILD-TYPE                         9   105
D30V4, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                           7                105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = XQ GAIN MUTATION ANALYSIS
D31V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED     4   0
  XQ GAIN WILD-TYPE 121   4
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4               125 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                0                 4 
$`XQ GAIN MUTATED`
TCGA-RW-A681 TCGA-SR-A6MT TCGA-WB-A80L TCGA-WB-A81A 
       23.80       106.75        22.29        12.20 

$`XQ GAIN WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 
       19.86         2.93         7.10        33.30         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
       13.32         1.22        11.70        13.05         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02         0.69         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        0.59        20.09        24.00        26.30        23.51        14.50 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       11.38        29.88        29.98        19.76        17.33        10.65 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD 
       11.77         6.08         7.89        12.20       104.55       101.49 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       70.65        67.07        98.07         9.01        99.06         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV 
        0.10        51.22        54.44        73.05       110.53       107.47 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        11.34        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
        7.96        10.42        25.32        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       19.86        12.03        12.49        16.60        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       10.65        27.62         4.47         4.73         4.21       303.09 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 
      127.56        29.16        19.59        32.88         5.98        17.46 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       32.61        26.14         7.69         0.79        37.18        24.00 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       24.23        42.54         1.12         1.87        19.56        21.44 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       46.22        12.99        24.82         1.61        11.74         9.47 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        56.52         1.35        92.78         6.90 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             12.2               0.1 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           106.75            303.09 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           23.045            14.500 
[1] "12.2 - 106.8 (23.0)" "0.1 - 303.1 (14.5)" 
[1] "hr="     "2.6e+07"
D31V2, continuous
D31V3, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    3  1
  XQ GAIN WILD-TYPE 70 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3    1
  XQ GAIN WILD-TYPE   70   55
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               3                70
  MALE                 1                55
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     0
  XQ GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                           0     4
  XQ GAIN WILD-TYPE                         9   108
D31V4, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      0                 9
  WHITE                                          4               108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = 1P LOSS MUTATION ANALYSIS
D32V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   77  1
  1P LOSS WILD-TYPE 48  3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               78                51 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                 3 
$`1P LOSS MUTATED`
TCGA-P7-A5NY TCGA-P8-A5KD TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QT-A5XK 
       31.46         2.27         7.89        81.70        28.01         6.94 
TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RM-A68T TCGA-RT-A6YA TCGA-RT-A6YC 
        0.72         2.30         0.79        38.73        41.06         8.09 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 
       86.89        19.86         7.10        33.30         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A7D0 
       13.32         1.22        11.70        13.05         7.96         1.78 
TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WX TCGA-S7-A7X0 
        0.59        26.30        11.38        29.88        11.77         6.08 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
        7.89        12.20        70.65        67.07        98.07         9.01 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT 
       99.06         1.41         0.10        54.44        73.05       106.75 
TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
      110.53        24.66        11.34         4.34        25.15         7.96 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD 
       14.20        17.16         1.18        19.86        12.03        12.49 
TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7UY TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       16.60        17.69        10.65         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D 
      303.09        29.16        17.46        26.14         7.69         0.79 
TCGA-WB-A81E TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81Q 
       37.18        24.23        42.54        19.56        21.44        24.82 
TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
        1.61         9.47        71.05        56.52         1.35        92.78 

$`1P LOSS WILD-TYPE`
TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XL 
       29.03         0.95         5.88         1.25        36.23         1.81 
TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RW-A67X 
       25.18         4.41         0.95         0.92        97.22         2.93 
TCGA-RW-A681 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
       23.80         6.28        72.79        15.02         0.69         4.41 
TCGA-RW-A8AZ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WT 
        2.89        20.09        24.00        23.51        14.50        29.98 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SR-A6MP 
       19.76        17.33        10.65       104.55       101.49        51.22 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HH 
      107.47         3.12        49.61        10.42        25.32        25.61 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
       27.62        22.29       127.56        19.59        32.88         5.98 
TCGA-WB-A817 TCGA-WB-A81A TCGA-WB-A81F TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81N 
       32.61        12.20        24.00         1.12         1.87        46.22 
TCGA-WB-A81P TCGA-WB-A81S TCGA-XG-A823 
       12.99        11.74         6.90 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.10              0.69 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           303.09            127.56 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           13.185            19.590 
[1] "0.1 - 303.1 (13.2)" "0.7 - 127.6 (19.6)"
[1] "hr=" "4.3"
D32V2, continuous
D32V3, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   44 34
  1P LOSS WILD-TYPE 29 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     44   34
  1P LOSS WILD-TYPE   29   22
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              44                29
  MALE                34                22
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  1     3
  1P LOSS WILD-TYPE                                0     1
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           4    68
  1P LOSS WILD-TYPE                         5    44
D32V4, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          3                 1
  BLACK OR AFRICAN AMERICAN                      4                 5
  WHITE                                         68                44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = 1Q LOSS MUTATION ANALYSIS
D33V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    17   0
  1Q LOSS WILD-TYPE 108   4
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               17               112 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                0                 4 
$`1Q LOSS MUTATED`
TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RM-A68T TCGA-RW-A688 TCGA-RW-A68A 
        0.72         2.30         0.79        38.73         1.22        13.05 
TCGA-RX-A8JQ TCGA-S7-A7WQ TCGA-S7-A7X1 TCGA-SP-A6QF TCGA-SR-A6MT TCGA-SR-A6MY 
        0.59        11.38         7.89        70.65       106.75        24.66 
TCGA-W2-A7H7 TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81K TCGA-WB-A821 
       17.16         0.79        37.18        19.56         1.35 

$`1Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA 
       25.18         4.41         0.95         0.92        97.22        41.06 
TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 
        8.09        86.89        19.86         2.93         7.10        33.30 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A689 TCGA-RW-A68B 
       23.80         1.05         0.85        13.32        11.70         7.96 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 
        6.28        72.79        15.02         0.69         4.41         1.78 
TCGA-RW-A8AZ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        2.89        20.09        24.00        26.30        23.51        14.50 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       29.88        29.98        19.76        17.33        10.65        11.77 
TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI 
        6.08        12.20       104.55       101.49        67.07        98.07 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
        9.01        99.06         1.41         0.10        51.22        54.44 
TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MZ TCGA-SR-A6N0 
       73.05       110.53       107.47         3.12        11.34        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        25.15         7.96        10.42        25.32        14.20 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF 
        1.18        19.86        12.03        12.49        16.60        17.69 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        10.65        27.62        22.29         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       303.09       127.56        29.16        19.59        32.88 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A 
        5.98        17.46        32.61        26.14         7.69        12.20 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81M 
       24.00        24.23        42.54         1.12         1.87        21.44 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       46.22        12.99        24.82         1.61        11.74         9.47 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 TCGA-XG-A823 
       71.05        56.52        92.78         6.90 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.59              0.10 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           106.75            303.09 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           11.380            16.965 
[1] "0.6 - 106.8 (11.4)" "0.1 - 303.1 (17.0)"
[1] "hr="     "7.7e+07"
D33V2, continuous
D33V3, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    8  9
  1Q LOSS WILD-TYPE 65 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      8    9
  1Q LOSS WILD-TYPE   65   47
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               8                65
  MALE                 9                47
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     1
  1Q LOSS WILD-TYPE                                1     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           2    14
  1Q LOSS WILD-TYPE                         7    98
D33V4, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                      2                 7
  WHITE                                         14                98
[1] 4 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 = 2P LOSS MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED     7   0
  2P LOSS WILD-TYPE 118   4
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                7               122 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                0                 4 
$`2P LOSS MUTATED`
TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RW-A68G TCGA-S7-A7X0 TCGA-W2-A7HB TCGA-WB-A815 
        2.30         0.79         0.69         6.08        19.86         5.98 
TCGA-WB-A821 
        1.35 

$`2P LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        0.72        25.18         4.41         0.95        38.73         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
       97.22        41.06         8.09        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        7.10        33.30        23.80         1.05         0.85        13.32 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D 
        1.22        11.70        13.05         7.96         6.28        72.79 
TCGA-RW-A68F TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
       15.02         4.41         1.78         2.89         0.59        20.09 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       24.00        26.30        23.51        14.50        11.38        29.88 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X1 
       29.98        19.76        17.33        10.65        11.77         7.89 
TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
       12.20       104.55       101.49        70.65        67.07        98.07 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
        9.01        99.06         1.41         0.10        51.22        54.44 
TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY 
       73.05       106.75       110.53       107.47         3.12        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       11.34        49.61         4.34        25.15         7.96        10.42 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD 
       25.32        14.20        17.16         1.18        12.03        12.49 
TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L 
       16.60        17.69        25.61        10.65        27.62        22.29 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       303.09       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
       19.59        32.88        17.46        32.61        26.14         7.69 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       12.20         0.79        37.18        24.00        24.23        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
        1.12         1.87        19.56        21.44        46.22        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        11.74         9.47        71.05        56.52 
TCGA-WB-A822 TCGA-XG-A823 
       92.78         6.90 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.69              0.10 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            19.86            303.09 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            2.300            17.245 
[1] "0.7 - 19.9 (2.3)"   "0.1 - 303.1 (17.2)"
[1] "hr="     "9300000"
D34V2, continuous
D34V3, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    4  3
  2P LOSS WILD-TYPE 69 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      4    3
  2P LOSS WILD-TYPE   69   53
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               4                69
  MALE                 3                53
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     0
  2P LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           1     6
  2P LOSS WILD-TYPE                         8   106
D34V4, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      1                 8
  WHITE                                          6               106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = 2Q LOSS MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED     7   1
  2Q LOSS WILD-TYPE 118   3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                8               121 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                 3 
$`2Q LOSS MUTATED`
TCGA-QT-A5XO TCGA-QT-A69Q TCGA-S7-A7X0 TCGA-SP-A6QC TCGA-SP-A6QG TCGA-SR-A6MX 
        2.30         0.79         6.08       104.55        67.07         3.12 
TCGA-W2-A7HB TCGA-WB-A821 
       19.86         1.35 

$`2Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        0.72        25.18         4.41         0.95        38.73         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
       97.22        41.06         8.09        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        7.10        33.30        23.80         1.05         0.85        13.32 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D 
        1.22        11.70        13.05         7.96         6.28        72.79 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       15.02         0.69         4.41         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       20.09        24.00        26.30        23.51        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       29.88        29.98        19.76        17.33        10.65        11.77 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ 
        7.89        12.20       101.49        70.65        98.07         9.01 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
       99.06         1.41         0.10        51.22        54.44        73.05 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
      106.75       110.53       107.47        24.66        11.34        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        25.15         7.96        10.42        25.32        14.20 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF 
       17.16         1.18        12.03        12.49        16.60        17.69 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        10.65        27.62        22.29         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       303.09       127.56        29.16        19.59        32.88 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A 
        5.98        17.46        32.61        26.14         7.69        12.20 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
        0.79        37.18        24.00        24.23        42.54         1.12 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
        1.87        19.56        21.44        46.22        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 
        1.61        11.74         9.47        71.05        56.52        92.78 
TCGA-XG-A823 
        6.90 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.79              0.10 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           104.55            303.09 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              4.6              16.6 
[1] "0.8 - 104.5 (4.6)"  "0.1 - 303.1 (16.6)"
[1] "hr=" "6.6"
D35V2, continuous
D35V3, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    4  4
  2Q LOSS WILD-TYPE 69 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      4    4
  2Q LOSS WILD-TYPE   69   52
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               4                69
  MALE                 4                52
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     0
  2Q LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           1     7
  2Q LOSS WILD-TYPE                         8   105
D35V4, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      1                 8
  WHITE                                          7               105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = 3P LOSS MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED   47  0
  3P LOSS WILD-TYPE 78  4
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               47                82 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                0                 4 
$`3P LOSS MUTATED`
TCGA-P8-A6RX TCGA-PR-A5PF TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XN 
        0.95         7.89        36.23         6.94         1.81        25.18 
TCGA-QT-A5XP TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
        4.41        97.22        41.06        19.86         2.93         7.10 
TCGA-RW-A680 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68C TCGA-RW-A7CZ 
       33.30         1.22        11.70        13.05         6.28         4.41 
TCGA-S7-A7WL TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7X0 
       20.09        14.50        11.38        29.88        29.98         6.08 
TCGA-S7-A7X1 TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SQ-A6I6 TCGA-SR-A6MT 
        7.89       101.49        67.07        98.07         0.10       106.75 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-TT-A6YK TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
      110.53       107.47        25.15        25.32        14.20        17.16 
TCGA-W2-A7HA TCGA-W2-A7HF TCGA-W2-A7UY TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A814 
        1.18        17.69        10.65       303.09        29.16        32.88 
TCGA-WB-A815 TCGA-WB-A819 TCGA-WB-A81W TCGA-WB-A821 TCGA-XG-A823 
        5.98         7.69        56.52         1.35         6.90 

$`3P LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RY TCGA-PR-A5PG TCGA-PR-A5PH 
       31.46        29.03         2.27         5.88        81.70        28.01 
TCGA-QR-A6GS TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
        1.25         0.72         2.30         0.79         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 
        0.92         8.09        86.89        23.80         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7D0 
       13.32         7.96        72.79        15.02         0.69         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WU 
        2.89         0.59        24.00        26.30        23.51        19.76 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QF 
       17.33        10.65        11.77        12.20       104.55        70.65 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
        9.01        99.06         1.41        51.22        54.44        73.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YN 
        3.12        24.66        11.34        49.61         4.34         7.96 
TCGA-TT-A6YO TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       10.42        19.86        12.03        12.49        16.60        25.61 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80Q 
       27.62        22.29         4.47         4.73         4.21       127.56 
TCGA-WB-A80Y TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D 
       19.59        17.46        32.61        26.14        12.20         0.79 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        24.00        24.23        42.54         1.12         1.87 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       19.56        21.44        46.22        12.99        24.82         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A822 
       11.74         9.47        71.05        92.78 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.10              0.59 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           303.09            127.56 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            14.50             15.81 
[1] "0.1 - 303.1 (14.5)" "0.6 - 127.6 (15.8)"
[1] "hr="     "4.1e+08"
D36V2, continuous
D36V3, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   30 17
  3P LOSS WILD-TYPE 43 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     30   17
  3P LOSS WILD-TYPE   43   39
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              30                43
  MALE                17                39
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  1     0
  3P LOSS WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                           6    39
  3P LOSS WILD-TYPE                         3    73
D36V4, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      6                 3
  WHITE                                         39                73
[1] 4 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 = 3Q LOSS MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED   69  1
  3Q LOSS WILD-TYPE 56  3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               70                59 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                 3 
$`3Q LOSS MUTATED`
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XN 
        2.27         0.95        36.23         6.94         0.72        25.18 
TCGA-QT-A5XP TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
        4.41        97.22        41.06        19.86         2.93         7.10 
TCGA-RW-A680 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
       33.30         0.85         1.22        11.70        13.05         7.96 
TCGA-RW-A68C TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-S7-A7WL TCGA-S7-A7WP TCGA-S7-A7WQ 
        6.28         4.41         1.78        20.09        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QD TCGA-SP-A6QF 
       29.88         6.08         7.89        12.20       101.49        70.65 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.07        98.07         9.01        99.06         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY 
       51.22       106.75       110.53       107.47         3.12        24.66 
TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       11.34         4.34        25.15        25.32        14.20        17.16 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HF TCGA-W2-A7UY 
        1.18        19.86        12.03        12.49        17.69        10.65 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A814 TCGA-WB-A816 
        4.47         4.73       303.09        29.16        32.88        17.46 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81R TCGA-WB-A81T 
       26.14         7.69        24.00        24.23         1.61         9.47 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       56.52         1.35        92.78         6.90 

$`3Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH 
       31.46        29.03         5.88         7.89        81.70        28.01 
TCGA-QR-A6GS TCGA-QT-A5XL TCGA-QT-A5XO TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
        1.25         1.81         2.30         0.79         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A686 
        0.92         8.09        86.89        23.80         1.05        13.32 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WM 
       72.79        15.02         0.69         2.89         0.59        24.00 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       26.30        23.51        29.98        19.76        17.33        10.65 
TCGA-S7-A7WX TCGA-SP-A6QC TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6N0 TCGA-TT-A6YN 
       11.77       104.55        54.44        73.05        49.61         7.96 
TCGA-TT-A6YO TCGA-W2-A7HE TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80O 
       10.42        16.60        25.61        27.62        22.29         4.21 
TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A817 TCGA-WB-A81A TCGA-WB-A81D 
      127.56        19.59         5.98        32.61        12.20         0.79 
TCGA-WB-A81E TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       37.18        42.54         1.12         1.87        19.56        21.44 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81S TCGA-WB-A81V 
       46.22        12.99        24.82        11.74        71.05 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.10              0.59 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           303.09            127.56 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            12.77             19.56 
[1] "0.1 - 303.1 (12.8)" "0.6 - 127.6 (19.6)"
[1] "hr=" "3.4"
D37V2, continuous
D37V3, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   41 29
  3Q LOSS WILD-TYPE 32 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     41   29
  3Q LOSS WILD-TYPE   32   27
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              41                32
  MALE                29                27
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  1     2
  3Q LOSS WILD-TYPE                                0     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           6    58
  3Q LOSS WILD-TYPE                         3    54
D37V4, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                 2
  BLACK OR AFRICAN AMERICAN                      6                 3
  WHITE                                         58                54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = 4P LOSS MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED     8   0
  4P LOSS WILD-TYPE 117   4
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                8               121 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                0                 4 
$`4P LOSS MUTATED`
TCGA-QR-A6GS TCGA-QT-A69Q TCGA-RT-A6YA TCGA-RW-A67X TCGA-RW-A68C TCGA-TT-A6YP 
        1.25         0.79        41.06         2.93         6.28        25.32 
TCGA-WB-A81J TCGA-WB-A821 
        1.87         1.35 

$`4P LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       81.70        28.01        36.23         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
       25.18         2.30         4.41         0.95        38.73         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A680 
       97.22         8.09        86.89        19.86         7.10        33.30 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 
       23.80         1.05         0.85        13.32         1.22        11.70 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
       13.05         7.96        72.79        15.02         0.69         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89         0.59        20.09        24.00        26.30 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       23.51        14.50        11.38        29.88        29.98        19.76 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       17.33        10.65        11.77         6.08         7.89        12.20 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      104.55       101.49        70.65        67.07        98.07         9.01 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
       99.06         1.41         0.10        51.22        54.44        73.05 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
      106.75       110.53       107.47         3.12        24.66        11.34 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7H5 
       49.61         4.34        25.15         7.96        10.42        14.20 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       17.16         1.18        19.86        12.03        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       17.69        25.61        10.65        27.62        22.29         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       303.09       127.56        29.16        19.59 
TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
       32.88         5.98        17.46        32.61        26.14         7.69 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       12.20         0.79        37.18        24.00        24.23        42.54 
TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
        1.12        19.56        21.44        46.22        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 
        1.61        11.74         9.47        71.05        56.52        92.78 
TCGA-XG-A823 
        6.90 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.79              0.10 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            41.06            303.09 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             2.40             17.16 
[1] "0.8 - 41.1 (2.4)"   "0.1 - 303.1 (17.2)"
[1] "hr="     "2.6e+07"
D38V2, continuous
D38V3, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    4  4
  4P LOSS WILD-TYPE 69 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      4    4
  4P LOSS WILD-TYPE   69   52
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               4                69
  MALE                 4                52
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     0
  4P LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                           0     8
  4P LOSS WILD-TYPE                         9   104
D38V4, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      0                 9
  WHITE                                          8               104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = 4Q LOSS MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED     8   0
  4Q LOSS WILD-TYPE 117   4
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                8               121 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                0                 4 
$`4Q LOSS MUTATED`
TCGA-QT-A69Q TCGA-RT-A6YA TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A68C TCGA-TT-A6YP 
        0.79        41.06        19.86         2.93         6.28        25.32 
TCGA-WB-A81J TCGA-WB-A821 
        1.87         1.35 

$`4Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T 
        0.72        25.18         2.30         4.41         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67Y TCGA-RW-A680 
        0.92        97.22         8.09        86.89         7.10        33.30 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 
       23.80         1.05         0.85        13.32         1.22        11.70 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
       13.05         7.96        72.79        15.02         0.69         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89         0.59        20.09        24.00        26.30 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       23.51        14.50        11.38        29.88        29.98        19.76 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       17.33        10.65        11.77         6.08         7.89        12.20 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      104.55       101.49        70.65        67.07        98.07         9.01 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
       99.06         1.41         0.10        51.22        54.44        73.05 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
      106.75       110.53       107.47         3.12        24.66        11.34 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7H5 
       49.61         4.34        25.15         7.96        10.42        14.20 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       17.16         1.18        19.86        12.03        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       17.69        25.61        10.65        27.62        22.29         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       303.09       127.56        29.16        19.59 
TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
       32.88         5.98        17.46        32.61        26.14         7.69 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       12.20         0.79        37.18        24.00        24.23        42.54 
TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
        1.12        19.56        21.44        46.22        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 
        1.61        11.74         9.47        71.05        56.52        92.78 
TCGA-XG-A823 
        6.90 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.79              0.10 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            41.06            303.09 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            4.605            16.600 
[1] "0.8 - 41.1 (4.6)"   "0.1 - 303.1 (16.6)"
[1] "hr="     "2.6e+07"
D39V2, continuous
D39V3, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    4  4
  4Q LOSS WILD-TYPE 69 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4    4
  4Q LOSS WILD-TYPE   69   52
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               4                69
  MALE                 4                52
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0     0
  4Q LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                           0     8
  4Q LOSS WILD-TYPE                         9   104
D39V4, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      0                 9
  WHITE                                          8               104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = 5P LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     4   0
  5P LOSS WILD-TYPE 121   4
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4               125 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                0                 4 
$`5P LOSS MUTATED`
TCGA-QT-A69Q TCGA-RW-A68C TCGA-W2-A7H7 TCGA-W2-A7UY 
        0.79         6.28        17.16        10.65 

$`5P LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T 
        0.72        25.18         2.30         4.41         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92        97.22        41.06         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 
        2.93         7.10        33.30        23.80         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68D 
       13.32         1.22        11.70        13.05         7.96        72.79 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       15.02         0.69         4.41         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       20.09        24.00        26.30        23.51        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       29.88        29.98        19.76        17.33        10.65        11.77 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
        6.08         7.89        12.20       104.55       101.49        70.65 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.07        98.07         9.01        99.06         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
       51.22        54.44        73.05       106.75       110.53       107.47 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        11.34        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HB 
        7.96        10.42        25.32        14.20         1.18        19.86 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-WB-A80K 
       12.03        12.49        16.60        17.69        25.61        27.62 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       22.29         4.47         4.73         4.21       303.09       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 
       29.16        19.59        32.88         5.98        17.46        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       26.14         7.69        12.20         0.79        37.18        24.00 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       24.23        42.54         1.12         1.87        19.56        21.44 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       46.22        12.99        24.82         1.61        11.74         9.47 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        56.52         1.35        92.78         6.90 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.79              0.10 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            17.16            303.09 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            8.465            16.600 
[1] "0.8 - 17.2 (8.5)"   "0.1 - 303.1 (16.6)"
[1] "hr="     "9300000"
D40V2, continuous
D40V3, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    1  3
  5P LOSS WILD-TYPE 72 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1    3
  5P LOSS WILD-TYPE   72   53
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               1                72
  MALE                 3                53
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     0
  5P LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           0     4
  5P LOSS WILD-TYPE                         9   108
D40V4, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      0                 9
  WHITE                                          4               108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = 5Q LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED     6   0
  5Q LOSS WILD-TYPE 119   4
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6               123 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                0                 4 
$`5Q LOSS MUTATED`
TCGA-QT-A5XJ TCGA-QT-A69Q TCGA-RW-A67Y TCGA-RW-A68C TCGA-WB-A80M TCGA-WB-A81W 
       36.23         0.79         7.10         6.28         4.47        56.52 

$`5Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       81.70        28.01         1.25         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
       25.18         2.30         4.41         0.95        38.73         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
       97.22        41.06         8.09        86.89        19.86         2.93 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
       33.30        23.80         1.05         0.85        13.32         1.22 
TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G 
       11.70        13.05         7.96        72.79        15.02         0.69 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89         0.59        20.09        24.00 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       26.30        23.51        14.50        11.38        29.88        29.98 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 
       19.76        17.33        10.65        11.77         6.08         7.89 
TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
       12.20       104.55       101.49        70.65        67.07        98.07 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
        9.01        99.06         1.41         0.10        51.22        54.44 
TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY 
       73.05       106.75       110.53       107.47         3.12        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       11.34        49.61         4.34        25.15         7.96        10.42 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC 
       25.32        14.20        17.16         1.18        19.86        12.03 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       12.49        16.60        17.69        25.61        10.65        27.62 
TCGA-WB-A80L TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
       22.29         4.73         4.21       303.09       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 
       19.59        32.88         5.98        17.46        32.61        26.14 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
        7.69        12.20         0.79        37.18        24.00        24.23 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54         1.12         1.87        19.56        21.44        46.22 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       12.99        24.82         1.61        11.74         9.47        71.05 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        1.35        92.78         6.90 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.79              0.10 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            56.52            303.09 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             6.69             16.60 
[1] "0.8 - 56.5 (6.7)"   "0.1 - 303.1 (16.6)"
[1] "hr="     "2.6e+07"
D41V2, continuous
D41V3, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    2  4
  5Q LOSS WILD-TYPE 71 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      2    4
  5Q LOSS WILD-TYPE   71   52
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               2                71
  MALE                 4                52
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  0     0
  5Q LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                           1     5
  5Q LOSS WILD-TYPE                         8   107
D41V4, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      1                 8
  WHITE                                          5               107
[1] 4 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 = 6Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    16   0
  6Q LOSS WILD-TYPE 109   4
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               16               113 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                0                 4 
$`6Q LOSS MUTATED`
TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QT-A5XN TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WR 
        2.27        81.70        25.18        24.00        26.30        29.88 
TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-W2-A7HC TCGA-W2-A7UY TCGA-WB-A80O TCGA-WB-A80V 
       24.66         4.34        12.03        10.65         4.21        29.16 
TCGA-WB-A819 TCGA-WB-A81R TCGA-WB-A81S TCGA-XG-A823 
        7.69         1.61        11.74         6.90 

$`6Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PH 
       31.46        29.03         0.95         5.88         7.89        28.01 
TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XO 
        1.25        36.23         6.94         1.81         0.72         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        4.41         0.79         0.95        38.73         0.92        97.22 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       41.06         8.09        86.89        19.86         2.93         7.10 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
       33.30        23.80         1.05         0.85        13.32         1.22 
TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F 
       11.70        13.05         7.96         6.28        72.79        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        0.69         4.41         1.78         2.89         0.59        20.09 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       23.51        14.50        11.38        29.98        19.76        17.33 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC 
       10.65        11.77         6.08         7.89        12.20       104.55 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      101.49        70.65        67.07        98.07         9.01        99.06 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT 
        1.41         0.10        51.22        54.44        73.05       106.75 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YK 
      110.53       107.47         3.12        11.34        49.61        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
        7.96        10.42        25.32        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-WB-A80K 
       19.86        12.49        16.60        17.69        25.61        27.62 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80Y 
       22.29         4.47         4.73       303.09       127.56        19.59 
TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A81A 
       32.88         5.98        17.46        32.61        26.14        12.20 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
        0.79        37.18        24.00        24.23        42.54         1.12 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
        1.87        19.56        21.44        46.22        12.99        24.82 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
        9.47        71.05        56.52         1.35        92.78 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             1.61              0.10 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            81.70            303.09 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           11.885            16.600 
[1] "1.6 - 81.7 (11.9)"  "0.1 - 303.1 (16.6)"
[1] "hr="     "8.1e+07"
D42V2, continuous
D42V3, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   12  4
  6Q LOSS WILD-TYPE 61 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     12    4
  6Q LOSS WILD-TYPE   61   52
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              12                61
  MALE                 4                52
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0     0
  6Q LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           1    14
  6Q LOSS WILD-TYPE                         8    98
D42V4, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      1                 8
  WHITE                                         14                98
[1] 4 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 = 7Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     4   0
  7Q LOSS WILD-TYPE 121   4
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               125 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                0                 4 
$`7Q LOSS MUTATED`
TCGA-QT-A5XK TCGA-SP-A6QF TCGA-SR-A6MQ TCGA-WB-A81N 
        6.94        70.65        54.44        46.22 

$`7Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A5XM 
       81.70        28.01         1.25        36.23         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
       25.18         2.30         4.41         0.79         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92        97.22        41.06         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 
        2.93         7.10        33.30        23.80         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
       13.32         1.22        11.70        13.05         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02         0.69         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        0.59        20.09        24.00        26.30        23.51        14.50 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       11.38        29.88        29.98        19.76        17.33        10.65 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD 
       11.77         6.08         7.89        12.20       104.55       101.49 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.07        98.07         9.01        99.06         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX 
       51.22        73.05       106.75       110.53       107.47         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        11.34        49.61         4.34        25.15         7.96 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
       10.42        25.32        14.20        17.16         1.18        19.86 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY 
       12.03        12.49        16.60        17.69        25.61        10.65 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       27.62        22.29         4.47         4.73         4.21       303.09 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 
      127.56        29.16        19.59        32.88         5.98        17.46 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        26.14         7.69        12.20         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       21.44        12.99        24.82         1.61        11.74         9.47 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        56.52         1.35        92.78         6.90 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             6.94              0.10 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            70.65            303.09 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            50.33             14.50 
[1] "6.9 - 70.7 (50.3)"  "0.1 - 303.1 (14.5)"
[1] "hr="     "2.6e+07"
D43V2, continuous
D43V3, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    3  1
  7Q LOSS WILD-TYPE 70 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    1
  7Q LOSS WILD-TYPE   70   55
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               3                70
  MALE                 1                55
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     2
  7Q LOSS WILD-TYPE                                1     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           1     1
  7Q LOSS WILD-TYPE                         8   111
D43V4, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 2
  BLACK OR AFRICAN AMERICAN                      1                 8
  WHITE                                          1               111
[1] 4 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 = 8P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    14   1
  8P LOSS WILD-TYPE 111   3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               15               114 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                 3 
$`8P LOSS MUTATED`
TCGA-PR-A5PF TCGA-PR-A5PG TCGA-RT-A6YA TCGA-RW-A68A TCGA-RW-A68D TCGA-S7-A7WR 
        7.89        81.70        41.06        13.05        72.79        29.88 
TCGA-S7-A7WT TCGA-SR-A6MT TCGA-W2-A7H5 TCGA-W2-A7HE TCGA-WB-A80V TCGA-WB-A81P 
       29.98       106.75        14.20        16.60        29.16        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T 
       24.82         1.61         9.47 

$`8P LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PH 
       31.46        29.03         2.27         0.95         5.88        28.01 
TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
        1.25        36.23         6.94         1.81         0.72        25.18 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        2.30         4.41         0.79         0.95        38.73         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       97.22         8.09        86.89        19.86         2.93         7.10 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
       33.30        23.80         1.05         0.85        13.32         1.22 
TCGA-RW-A689 TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
       11.70         7.96         6.28        15.02         0.69         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89         0.59        20.09        24.00        26.30 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       23.51        14.50        11.38        19.76        17.33        10.65 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD 
       11.77         6.08         7.89        12.20       104.55       101.49 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       70.65        67.07        98.07         9.01        99.06         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV 
        0.10        51.22        54.44        73.05       110.53       107.47 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        11.34        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
        7.96        10.42        25.32        17.16         1.18        19.86 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       12.03        12.49        17.69        25.61        10.65        27.62 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       22.29         4.47         4.73         4.21       303.09       127.56 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 
       19.59        32.88         5.98        17.46        32.61        26.14 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
        7.69        12.20         0.79        37.18        24.00        24.23 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54         1.12         1.87        19.56        21.44        46.22 
TCGA-WB-A81S TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       11.74        71.05        56.52         1.35        92.78         6.90 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             1.61              0.10 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           106.75            303.09 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            24.82             13.91 
[1] "1.6 - 106.8 (24.8)" "0.1 - 303.1 (13.9)"
[1] "hr=" "2"  
D44V2, continuous
D44V3, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   11  4
  8P LOSS WILD-TYPE 62 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     11    4
  8P LOSS WILD-TYPE   62   52
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              11                62
  MALE                 4                52
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  0     1
  8P LOSS WILD-TYPE                                1     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                           0    14
  8P LOSS WILD-TYPE                         9    98
D44V4, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                      0                 9
  WHITE                                         14                98
[1] 4 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 = 8Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     8   1
  8Q LOSS WILD-TYPE 117   3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               120 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                 3 
$`8Q LOSS MUTATED`
TCGA-RW-A68A TCGA-S7-A7WR TCGA-SR-A6MT TCGA-SR-A6MX TCGA-W2-A7H5 TCGA-W2-A7H7 
       13.05        29.88       106.75         3.12        14.20        17.16 
TCGA-W2-A7HD TCGA-WB-A80K TCGA-WB-A80V 
       12.49        27.62        29.16 

$`8Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       19.86         2.93         7.10        33.30        23.80         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68B TCGA-RW-A68C 
        0.85        13.32         1.22        11.70         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02         0.69         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        0.59        20.09        24.00        26.30        23.51        14.50 
TCGA-S7-A7WQ TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       11.38        29.98        19.76        17.33        10.65        11.77 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
        6.08         7.89        12.20       104.55       101.49        70.65 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.07        98.07         9.01        99.06         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MY 
       51.22        54.44        73.05       110.53       107.47        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       11.34        49.61         4.34        25.15         7.96        10.42 
TCGA-TT-A6YP TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HE TCGA-W2-A7HF 
       25.32         1.18        19.86        12.03        16.60        17.69 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       25.61        10.65        22.29         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 
      303.09       127.56        19.59        32.88         5.98        17.46 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        26.14         7.69        12.20         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       21.44        46.22        12.99        24.82         1.61        11.74 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        9.47        71.05        56.52         1.35        92.78         6.90 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             3.12              0.10 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           106.75            303.09 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            17.16             14.76 
[1] "3.1 - 106.8 (17.2)" "0.1 - 303.1 (14.8)"
[1] "hr=" "3.7"
D45V2, continuous
D45V3, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    6  3
  8Q LOSS WILD-TYPE 67 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6    3
  8Q LOSS WILD-TYPE   67   53
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               6                67
  MALE                 3                53
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     0
  8Q LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           0     9
  8Q LOSS WILD-TYPE                         9   103
D45V4, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      0                 9
  WHITE                                          9               103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = 9P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED     6   1
  9P LOSS WILD-TYPE 119   3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                7               122 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                1                 3 
$`9P LOSS MUTATED`
TCGA-QT-A5XP TCGA-RT-A6YA TCGA-SP-A6QJ TCGA-SR-A6MV TCGA-W2-A7H5 TCGA-WB-A81Q 
        4.41        41.06         9.01       107.47        14.20        24.82 
TCGA-WB-A81R 
        1.61 

$`9P LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
        0.72        25.18         2.30         0.79         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
        0.92        97.22         8.09        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        7.10        33.30        23.80         1.05         0.85        13.32 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D 
        1.22        11.70        13.05         7.96         6.28        72.79 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       15.02         0.69         4.41         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       20.09        24.00        26.30        23.51        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       29.88        29.98        19.76        17.33        10.65        11.77 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
        6.08         7.89        12.20       104.55       101.49        70.65 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
       67.07        98.07        99.06         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MX TCGA-SR-A6MY 
       54.44        73.05       106.75       110.53         3.12        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       11.34        49.61         4.34        25.15         7.96        10.42 
TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD 
       25.32        17.16         1.18        19.86        12.03        12.49 
TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L 
       16.60        17.69        25.61        10.65        27.62        22.29 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       303.09       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 
       19.59        32.88         5.98        17.46        32.61        26.14 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
        7.69        12.20         0.79        37.18        24.00        24.23 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54         1.12         1.87        19.56        21.44        46.22 
TCGA-WB-A81P TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 
       12.99        11.74         9.47        71.05        56.52         1.35 
TCGA-WB-A822 TCGA-XG-A823 
       92.78         6.90 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             1.61              0.10 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           107.47            303.09 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            14.20             15.81 
[1] "1.6 - 107.5 (14.2)" "0.1 - 303.1 (15.8)"
[1] "hr=" "5.4"
D46V2, continuous
D46V3, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    6  1
  9P LOSS WILD-TYPE 67 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6    1
  9P LOSS WILD-TYPE   67   55
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               6                67
  MALE                 1                55
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0     0
  9P LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                           1     6
  9P LOSS WILD-TYPE                         8   106
D46V4, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      1                 8
  WHITE                                          6               106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = 9Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED     7   1
  9Q LOSS WILD-TYPE 118   3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                8               121 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                1                 3 
$`9Q LOSS MUTATED`
TCGA-QT-A5XJ TCGA-QT-A5XP TCGA-RT-A6YA TCGA-SR-A6MP TCGA-SR-A6MV TCGA-W2-A7H5 
       36.23         4.41        41.06        51.22       107.47        14.20 
TCGA-W2-A7H7 TCGA-WB-A81Q 
       17.16        24.82 

$`9Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       81.70        28.01         1.25         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
       25.18         2.30         0.79         0.95        38.73         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       97.22         8.09        86.89        19.86         2.93         7.10 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
       33.30        23.80         1.05         0.85        13.32         1.22 
TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F 
       11.70        13.05         7.96         6.28        72.79        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        0.69         4.41         1.78         2.89         0.59        20.09 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       24.00        26.30        23.51        14.50        11.38        29.88 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       29.98        19.76        17.33        10.65        11.77         6.08 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
        7.89        12.20       104.55       101.49        70.65        67.07 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MQ 
       98.07         9.01        99.06         1.41         0.10        54.44 
TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
       73.05       106.75       110.53         3.12        24.66        11.34 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15         7.96        10.42        25.32 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF 
        1.18        19.86        12.03        12.49        16.60        17.69 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        10.65        27.62        22.29         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       303.09       127.56        29.16        19.59        32.88 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A 
        5.98        17.46        32.61        26.14         7.69        12.20 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
        0.79        37.18        24.00        24.23        42.54         1.12 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R 
        1.87        19.56        21.44        46.22        12.99         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       11.74         9.47        71.05        56.52         1.35        92.78 
TCGA-XG-A823 
        6.90 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             4.41              0.10 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           107.47            303.09 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           30.525            13.320 
[1] "4.4 - 107.5 (30.5)" "0.1 - 303.1 (13.3)"
[1] "hr=" "3.5"
D47V2, continuous
D47V3, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    6  2
  9Q LOSS WILD-TYPE 67 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      6    2
  9Q LOSS WILD-TYPE   67   54
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               6                67
  MALE                 2                54
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     0
  9Q LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           2     6
  9Q LOSS WILD-TYPE                         7   106
D47V4, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 4
  BLACK OR AFRICAN AMERICAN                      2                 7
  WHITE                                          6               106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = 11P LOSS MUTATION ANALYSIS
D48V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   40  1
  11P LOSS WILD-TYPE 85  3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                41                 88 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                  3 
$`11P LOSS MUTATED`
TCGA-P8-A6RX TCGA-P8-A6RY TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6YA 
        0.95         5.88         0.95        38.73         0.92        41.06 
TCGA-RW-A67X TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A68A TCGA-RW-A68C TCGA-RW-A68F 
        2.93        23.80         1.05        13.05         6.28        15.02 
TCGA-RW-A7CZ TCGA-RW-A8AZ TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7WW 
        4.41         2.89        14.50        11.38        19.76        10.65 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-SP-A6QD TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6N0 
        6.08         7.89       101.49       106.75       110.53        49.61 
TCGA-TT-A6YK TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7UY TCGA-WB-A80M TCGA-WB-A815 
       25.15        25.32        17.16        10.65         4.47         5.98 
TCGA-WB-A816 TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81P TCGA-WB-A81S 
       17.46         1.12        19.56        21.44        12.99        11.74 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        56.52         1.35        92.78         6.90 

$`11P LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH 
       31.46        29.03         2.27         7.89        81.70        28.01 
TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
        1.25        36.23         6.94         1.81         0.72        25.18 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V 
        2.30         4.41         0.79        97.22         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
       19.86         7.10        33.30         0.85        13.32         1.22 
TCGA-RW-A689 TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A68G TCGA-RW-A7D0 TCGA-RX-A8JQ 
       11.70         7.96        72.79         0.69         1.78         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WR TCGA-S7-A7WT 
       20.09        24.00        26.30        23.51        29.88        29.98 
TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QG 
       17.33        11.77        12.20       104.55        70.65        67.07 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
       98.07         9.01        99.06         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
       54.44        73.05       107.47         3.12        24.66        11.34 
TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HB 
        4.34         7.96        10.42        14.20         1.18        19.86 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-WB-A80K 
       12.03        12.49        16.60        17.69        25.61        27.62 
TCGA-WB-A80L TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
       22.29         4.73         4.21       303.09       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A 
       19.59        32.88        32.61        26.14         7.69        12.20 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81J 
        0.79        37.18        24.00        24.23        42.54         1.87 
TCGA-WB-A81N TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T 
       46.22        24.82         1.61         9.47 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.92               0.10 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            110.53             303.09 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             12.99              18.64 
[1] "0.9 - 110.5 (13.0)" "0.1 - 303.1 (18.6)"
[1] "hr=" "1.2"
D48V2, continuous
D48V3, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   21 20
  11P LOSS WILD-TYPE 52 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     21   20
  11P LOSS WILD-TYPE   52   36
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               21                 52
  MALE                 20                 36
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     0
  11P LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           1    39
  11P LOSS WILD-TYPE                         8    73
D48V4, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       1                  8
  WHITE                                          39                 73
[1] 4 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 = 11Q LOSS MUTATION ANALYSIS
D49V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   33  1
  11Q LOSS WILD-TYPE 92  3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                34                 95 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                  3 
$`11Q LOSS MUTATED`
TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-QR-A6GS TCGA-QT-A5XL TCGA-QT-A5XO 
        0.95         5.88         7.89         1.25         1.81         2.30 
TCGA-QT-A69Q TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6YA TCGA-RW-A67X TCGA-RW-A681 
        0.79        38.73         0.92        41.06         2.93        23.80 
TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68F TCGA-RW-A7CZ TCGA-RW-A8AZ TCGA-S7-A7WP 
       11.70         6.28        15.02         4.41         2.89        14.50 
TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-SR-A6MT 
       11.38        19.76        10.65         6.08         7.89       106.75 
TCGA-SR-A6N0 TCGA-TT-A6YP TCGA-W2-A7UY TCGA-WB-A815 TCGA-WB-A81P TCGA-WB-A81S 
       49.61        25.32        10.65         5.98        12.99        11.74 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-XG-A823 
       71.05        56.52         1.35         6.90 

$`11Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QT-A5XJ 
       31.46        29.03         2.27        81.70        28.01        36.23 
TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RT-A6Y9 
        6.94         0.72        25.18         4.41         0.95        97.22 
TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 
        8.09        86.89        19.86         7.10        33.30         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68D 
        0.85        13.32         1.22        13.05         7.96        72.79 
TCGA-RW-A68G TCGA-RW-A7D0 TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        0.69         1.78         0.59        20.09        24.00        26.30 
TCGA-S7-A7WO TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X2 
       23.51        29.88        29.98        17.33        11.77        12.20 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      104.55       101.49        70.65        67.07        98.07         9.01 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
       99.06         1.41         0.10        51.22        54.44        73.05 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ 
      110.53       107.47         3.12        24.66        11.34         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       25.15         7.96        10.42        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       19.86        12.03        12.49        16.60        17.69        25.61 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       27.62        22.29         4.47         4.73         4.21       303.09 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A817 
      127.56        29.16        19.59        32.88        17.46        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       26.14         7.69        12.20         0.79        37.18        24.00 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       24.23        42.54         1.12         1.87        19.56        21.44 
TCGA-WB-A81N TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A822 
       46.22        24.82         1.61         9.47        92.78 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.79               0.10 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            106.75             303.09 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              9.27              19.86 
[1] "0.8 - 106.8 (9.3)"  "0.1 - 303.1 (19.9)"
[1] "hr=" "1.3"
D49V2, continuous
D49V3, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   19 15
  11Q LOSS WILD-TYPE 54 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     19   15
  11Q LOSS WILD-TYPE   54   41
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               19                 54
  MALE                 15                 41
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     0
  11Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           2    32
  11Q LOSS WILD-TYPE                         7    80
D49V4, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       2                  7
  WHITE                                          32                 80
[1] 4 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 = 13Q LOSS MUTATION ANALYSIS
D50V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED     6   0
  13Q LOSS WILD-TYPE 119   4
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 6                123 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 0                  4 
$`13Q LOSS MUTATED`
TCGA-PR-A5PF TCGA-QT-A5XP TCGA-RW-A68A TCGA-S7-A7WX TCGA-SP-A6QF TCGA-W2-A7H5 
        7.89         4.41        13.05        11.77        70.65        14.20 

$`13Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG 
       31.46        29.03         2.27         0.95         5.88        81.70 
TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       28.01         1.25        36.23         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
       25.18         2.30         0.79         0.95        38.73         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
       97.22        41.06         8.09        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        7.10        33.30        23.80         1.05         0.85        13.32 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F 
        1.22        11.70         7.96         6.28        72.79        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        0.69         4.41         1.78         2.89         0.59        20.09 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       24.00        26.30        23.51        14.50        11.38        29.88 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X1 
       29.98        19.76        17.33        10.65         6.08         7.89 
TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
       12.20       104.55       101.49        67.07        98.07         9.01 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
       99.06         1.41         0.10        51.22        54.44        73.05 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
      106.75       110.53       107.47         3.12        24.66        11.34 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15         7.96        10.42        25.32 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       17.16         1.18        19.86        12.03        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       17.69        25.61        10.65        27.62        22.29         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       303.09       127.56        29.16        19.59 
TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
       32.88         5.98        17.46        32.61        26.14         7.69 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       12.20         0.79        37.18        24.00        24.23        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
        1.12         1.87        19.56        21.44        46.22        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        11.74         9.47        71.05        56.52 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        1.35        92.78         6.90 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              4.41               0.10 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             70.65             303.09 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             12.41              17.16 
[1] "4.4 - 70.7 (12.4)"  "0.1 - 303.1 (17.2)"
[1] "hr="     "2.6e+07"
D50V2, continuous
D50V3, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    4  2
  13Q LOSS WILD-TYPE 69 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4    2
  13Q LOSS WILD-TYPE   69   54
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                4                 69
  MALE                  2                 54
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  0     1
  13Q LOSS WILD-TYPE                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                           1     4
  13Q LOSS WILD-TYPE                         8   108
D50V4, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                       1                  8
  WHITE                                           4                108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = 14Q LOSS MUTATION ANALYSIS
D51V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    16   0
  14Q LOSS WILD-TYPE 109   4
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                16                113 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 0                  4 
$`14Q LOSS MUTATED`
TCGA-PR-A5PH TCGA-QT-A69Q TCGA-RT-A6YA TCGA-RW-A67X TCGA-RW-A689 TCGA-RW-A68C 
       28.01         0.79        41.06         2.93        11.70         6.28 
TCGA-S7-A7WR TCGA-S7-A7WV TCGA-SR-A6MS TCGA-SR-A6MV TCGA-W2-A7H5 TCGA-W2-A7HF 
       29.88        17.33        73.05       107.47        14.20        17.69 
TCGA-WB-A815 TCGA-WB-A81K TCGA-WB-A81S TCGA-WB-A821 
        5.98        19.56        11.74         1.35 

$`14Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       81.70         1.25        36.23         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
       25.18         2.30         4.41         0.95        38.73         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A680 
       97.22         8.09        86.89        19.86         7.10        33.30 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68A 
       23.80         1.05         0.85        13.32         1.22        13.05 
TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 
        7.96        72.79        15.02         0.69         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89         0.59        20.09        24.00        26.30        23.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WW TCGA-S7-A7WX 
       14.50        11.38        29.98        19.76        10.65        11.77 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
        6.08         7.89        12.20       104.55       101.49        70.65 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.07        98.07         9.01        99.06         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MX TCGA-SR-A6MY 
       51.22        54.44       106.75       110.53         3.12        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       11.34        49.61         4.34        25.15         7.96        10.42 
TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD 
       25.32        17.16         1.18        19.86        12.03        12.49 
TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       16.60        25.61        10.65        27.62        22.29         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       303.09       127.56        29.16        19.59 
TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A 
       32.88        17.46        32.61        26.14         7.69        12.20 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
        0.79        37.18        24.00        24.23        42.54         1.12 
TCGA-WB-A81J TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
        1.87        21.44        46.22        12.99        24.82         1.61 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 TCGA-XG-A823 
        9.47        71.05        56.52        92.78         6.90 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.79               0.10 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            107.47             303.09 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            15.765             15.020 
[1] "0.8 - 107.5 (15.8)" "0.1 - 303.1 (15.0)"
[1] "hr="   "8e+07"
D51V2, continuous
D51V3, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   10  6
  14Q LOSS WILD-TYPE 63 50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     10    6
  14Q LOSS WILD-TYPE   63   50
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               10                 63
  MALE                  6                 50
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0     0
  14Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                           1    15
  14Q LOSS WILD-TYPE                         8    97
D51V4, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       1                  8
  WHITE                                          15                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = 15Q LOSS MUTATION ANALYSIS
D52V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED     3   0
  15Q LOSS WILD-TYPE 122   4
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 3                126 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 0                  4 
$`15Q LOSS MUTATED`
TCGA-SR-A6MQ TCGA-SR-A6MV TCGA-W2-A7HF 
       54.44       107.47        17.69 

$`15Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       19.86         2.93         7.10        33.30        23.80         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        0.85        13.32         1.22        11.70        13.05         7.96 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 
        6.28        72.79        15.02         0.69         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89         0.59        20.09        24.00        26.30        23.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       14.50        11.38        29.88        29.98        19.76        17.33 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC 
       10.65        11.77         6.08         7.89        12.20       104.55 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      101.49        70.65        67.07        98.07         9.01        99.06 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
        1.41         0.10        51.22        73.05       106.75       110.53 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        11.34        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
        7.96        10.42        25.32        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY 
       19.86        12.03        12.49        16.60        25.61        10.65 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       27.62        22.29         4.47         4.73         4.21       303.09 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 
      127.56        29.16        19.59        32.88         5.98        17.46 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        26.14         7.69        12.20         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       21.44        46.22        12.99        24.82         1.61        11.74 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        9.47        71.05        56.52         1.35        92.78         6.90 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             17.69               0.10 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            107.47             303.09 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             54.44              14.35 
[1] "17.7 - 107.5 (54.4)" "0.1 - 303.1 (14.3)" 
[1] "hr="     "2.6e+07"
D52V2, continuous
D52V3, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    3  0
  15Q LOSS WILD-TYPE 70 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3    0
  15Q LOSS WILD-TYPE   70   56
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                3                 70
  MALE                  0                 56
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0     1
  15Q LOSS WILD-TYPE                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           1     1
  15Q LOSS WILD-TYPE                         8   111
D52V4, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                       1                  8
  WHITE                                           1                111
[1] 4 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 = 16P LOSS MUTATION ANALYSIS
D53V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     4   2
  16P LOSS WILD-TYPE 121   2
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                123 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                  2 
$`16P LOSS MUTATED`
TCGA-PR-A5PF TCGA-QT-A69Q TCGA-SR-A6MT TCGA-SR-A6MX TCGA-WB-A81Q TCGA-WB-A81S 
        7.89         0.79       106.75         3.12        24.82        11.74 

$`16P LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG 
       31.46        29.03         2.27         0.95         5.88        81.70 
TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       28.01         1.25        36.23         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
       25.18         2.30         4.41         0.95        38.73         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
       97.22        41.06         8.09        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        7.10        33.30        23.80         1.05         0.85        13.32 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D 
        1.22        11.70        13.05         7.96         6.28        72.79 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       15.02         0.69         4.41         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       20.09        24.00        26.30        23.51        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       29.88        29.98        19.76        17.33        10.65        11.77 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
        6.08         7.89        12.20       104.55       101.49        70.65 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.07        98.07         9.01        99.06         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MY 
       51.22        54.44        73.05       110.53       107.47        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       11.34        49.61         4.34        25.15         7.96        10.42 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC 
       25.32        14.20        17.16         1.18        19.86        12.03 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       12.49        16.60        17.69        25.61        10.65        27.62 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       22.29         4.47         4.73         4.21       303.09       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 
       29.16        19.59        32.88         5.98        17.46        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       26.14         7.69        12.20         0.79        37.18        24.00 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       24.23        42.54         1.12         1.87        19.56        21.44 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       46.22        12.99         1.61         9.47        71.05        56.52 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        1.35        92.78         6.90 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.79               0.10 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            106.75             303.09 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             9.815             16.600 
[1] "0.8 - 106.8 (9.8)"  "0.1 - 303.1 (16.6)"
[1] "hr=" "22" 
D53V2, continuous
D53V3, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    3  3
  16P LOSS WILD-TYPE 70 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    3
  16P LOSS WILD-TYPE   70   53
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                3                 70
  MALE                  3                 53
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     0
  16P LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           0     6
  16P LOSS WILD-TYPE                         9   106
D53V4, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                           6                106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = 16Q LOSS MUTATION ANALYSIS
D54V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED     4   0
  16Q LOSS WILD-TYPE 121   4
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                125 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 0                  4 
$`16Q LOSS MUTATED`
TCGA-PR-A5PF TCGA-QT-A69Q TCGA-SR-A6MT TCGA-WB-A81S 
        7.89         0.79       106.75        11.74 

$`16Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG 
       31.46        29.03         2.27         0.95         5.88        81.70 
TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       28.01         1.25        36.23         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
       25.18         2.30         4.41         0.95        38.73         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
       97.22        41.06         8.09        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        7.10        33.30        23.80         1.05         0.85        13.32 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D 
        1.22        11.70        13.05         7.96         6.28        72.79 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       15.02         0.69         4.41         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       20.09        24.00        26.30        23.51        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       29.88        29.98        19.76        17.33        10.65        11.77 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
        6.08         7.89        12.20       104.55       101.49        70.65 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.07        98.07         9.01        99.06         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX 
       51.22        54.44        73.05       110.53       107.47         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        11.34        49.61         4.34        25.15         7.96 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
       10.42        25.32        14.20        17.16         1.18        19.86 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY 
       12.03        12.49        16.60        17.69        25.61        10.65 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       27.62        22.29         4.47         4.73         4.21       303.09 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 
      127.56        29.16        19.59        32.88         5.98        17.46 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        26.14         7.69        12.20         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T 
       21.44        46.22        12.99        24.82         1.61         9.47 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        56.52         1.35        92.78         6.90 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.79               0.10 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            106.75             303.09 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             9.815             16.600 
[1] "0.8 - 106.8 (9.8)"  "0.1 - 303.1 (16.6)"
[1] "hr="     "2.5e+07"
D54V2, continuous
D54V3, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    3  1
  16Q LOSS WILD-TYPE 70 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    1
  16Q LOSS WILD-TYPE   70   55
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                3                 70
  MALE                  1                 55
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     0
  16Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           0     4
  16Q LOSS WILD-TYPE                         9   108
D54V4, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                           4                108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = 17P LOSS MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   48  2
  17P LOSS WILD-TYPE 77  2
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                50                 79 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                  2 
$`17P LOSS MUTATED`
TCGA-PR-A5PG TCGA-QR-A6GS TCGA-QT-A5XN TCGA-QT-A69Q TCGA-RW-A67X TCGA-RW-A67Y 
       81.70         1.25        25.18         0.79         2.93         7.10 
TCGA-RW-A681 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68C 
       23.80         0.85         1.22        11.70        13.05         6.28 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7D0 TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WQ 
       15.02         0.69         1.78        20.09        24.00        11.38 
TCGA-S7-A7WT TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QD 
       29.98        10.65        11.77         7.89        12.20       101.49 
TCGA-SP-A6QJ TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MT TCGA-TT-A6YJ TCGA-TT-A6YK 
        9.01         0.10        54.44       106.75         4.34        25.15 
TCGA-TT-A6YN TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7UY TCGA-WB-A80N TCGA-WB-A80O 
        7.96         1.18        12.03        10.65         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A818 TCGA-WB-A81J 
      303.09        29.16        19.59         5.98        26.14         1.87 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81S TCGA-WB-A81T 
       21.44        46.22        12.99        24.82        11.74         9.47 
TCGA-WB-A81W TCGA-WB-A822 
       56.52        92.78 

$`17P LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PH TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XO 
       28.01        36.23         6.94         1.81         0.72         2.30 
TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA 
        4.41         0.95        38.73         0.92        97.22        41.06 
TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A686 
        8.09        86.89        19.86        33.30         1.05        13.32 
TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A7CZ TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WN 
        7.96        72.79         4.41         2.89         0.59        26.30 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7X0 
       23.51        14.50        29.88        19.76        17.33         6.08 
TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QK TCGA-SQ-A6I4 
      104.55        70.65        67.07        98.07        99.06         1.41 
TCGA-SR-A6MP TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY 
       51.22        73.05       110.53       107.47         3.12        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       11.34        49.61        10.42        25.32        14.20        17.16 
TCGA-W2-A7HB TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-WB-A80K 
       19.86        12.49        16.60        17.69        25.61        27.62 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80Q TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A817 
       22.29         4.47       127.56        32.88        17.46        32.61 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
        7.69        12.20         0.79        37.18        24.00        24.23 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81R TCGA-WB-A81V TCGA-WB-A821 
       42.54         1.12        19.56         1.61        71.05         1.35 
TCGA-XG-A823 
        6.90 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.10               0.59 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            303.09             127.56 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            11.755             19.560 
[1] "0.1 - 303.1 (11.8)" "0.6 - 127.6 (19.6)"
[1] "hr=" "1.8"
D55V2, continuous
D55V3, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   25 25
  17P LOSS WILD-TYPE 48 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     25   25
  17P LOSS WILD-TYPE   48   31
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               25                 48
  MALE                 25                 31
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  1     1
  17P LOSS WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                           1    45
  17P LOSS WILD-TYPE                         8    67
D55V4, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                       1                  8
  WHITE                                          45                 67
[1] 4 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 = 17Q LOSS MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    15   1
  17Q LOSS WILD-TYPE 110   3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                16                113 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                  3 
$`17Q LOSS MUTATED`
TCGA-QR-A6GS TCGA-QT-A5XN TCGA-QT-A69Q TCGA-RT-A6YA TCGA-RW-A67X TCGA-RW-A67Y 
        1.25        25.18         0.79        41.06         2.93         7.10 
TCGA-RW-A688 TCGA-RW-A68C TCGA-S7-A7WM TCGA-S7-A7WQ TCGA-S7-A7X1 TCGA-SQ-A6I6 
        1.22         6.28        24.00        11.38         7.89         0.10 
TCGA-SR-A6MT TCGA-WB-A80P TCGA-WB-A81N TCGA-WB-A81Q 
      106.75       303.09        46.22        24.82 

$`17Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       81.70        28.01        36.23         6.94         1.81         0.72 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        2.30         4.41         0.95        38.73         0.92        97.22 
TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
        8.09        86.89        19.86        33.30        23.80         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68D 
        0.85        13.32        11.70        13.05         7.96        72.79 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       15.02         0.69         4.41         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT 
       20.09        26.30        23.51        14.50        29.88        29.98 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 
       19.76        17.33        10.65        11.77         6.08        12.20 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      104.55       101.49        70.65        67.07        98.07         9.01 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU 
       99.06         1.41        51.22        54.44        73.05       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      107.47         3.12        24.66        11.34        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       25.15         7.96        10.42        25.32        14.20        17.16 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF 
        1.18        19.86        12.03        12.49        16.60        17.69 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        10.65        27.62        22.29         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
        4.21       127.56        29.16        19.59        32.88         5.98 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
       17.46        32.61        26.14         7.69        12.20         0.79 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        24.00        24.23        42.54         1.12         1.87 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       19.56        21.44        12.99         1.61        11.74         9.47 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        56.52         1.35        92.78         6.90 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.10               0.59 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            303.09             127.56 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             9.635             16.600 
[1] "0.1 - 303.1 (9.6)"  "0.6 - 127.6 (16.6)"
[1] "hr=" "2.5"
D56V2, continuous
D56V3, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    7  9
  17Q LOSS WILD-TYPE 66 47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      7    9
  17Q LOSS WILD-TYPE   66   47
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                7                 66
  MALE                  9                 47
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  0     0
  17Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           1    15
  17Q LOSS WILD-TYPE                         8    97
D56V4, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       1                  8
  WHITE                                          15                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = 18P LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    10   0
  18P LOSS WILD-TYPE 115   4
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                10                119 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 0                  4 
$`18P LOSS MUTATED`
TCGA-P8-A5KD TCGA-RW-A67X TCGA-RW-A68G TCGA-S7-A7X2 TCGA-SP-A6QF TCGA-W2-A7H7 
        2.27         2.93         0.69        12.20        70.65        17.16 
TCGA-WB-A80O TCGA-WB-A819 TCGA-WB-A81W TCGA-WB-A821 
        4.21         7.69        56.52         1.35 

$`18P LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       31.46        29.03         0.95         5.88         7.89        81.70 
TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       28.01         1.25        36.23         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
       25.18         2.30         4.41         0.79         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92        97.22        41.06         8.09        86.89        19.86 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        7.10        33.30        23.80         1.05         0.85        13.32 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D 
        1.22        11.70        13.05         7.96         6.28        72.79 
TCGA-RW-A68F TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
       15.02         4.41         1.78         2.89         0.59        20.09 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       24.00        26.30        23.51        14.50        11.38        29.88 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       29.98        19.76        17.33        10.65        11.77         6.08 
TCGA-S7-A7X1 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
        7.89       104.55       101.49        67.07        98.07         9.01 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
       99.06         1.41         0.10        51.22        54.44        73.05 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
      106.75       110.53       107.47         3.12        24.66        11.34 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15         7.96        10.42        25.32 
TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       14.20         1.18        19.86        12.03        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       17.69        25.61        10.65        27.62        22.29         4.47 
TCGA-WB-A80N TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.73       303.09       127.56        29.16        19.59        32.88 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D 
        5.98        17.46        32.61        26.14        12.20         0.79 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        24.00        24.23        42.54         1.12         1.87 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       19.56        21.44        46.22        12.99        24.82         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A822 TCGA-XG-A823 
       11.74         9.47        71.05        92.78         6.90 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.69               0.10 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             70.65             303.09 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              5.95              17.33 
[1] "0.7 - 70.7 (6.0)"   "0.1 - 303.1 (17.3)"
[1] "hr="     "2.6e+07"
D57V2, continuous
D57V3, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    4  6
  18P LOSS WILD-TYPE 69 50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4    6
  18P LOSS WILD-TYPE   69   50
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                4                 69
  MALE                  6                 50
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0     1
  18P LOSS WILD-TYPE                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                           0     9
  18P LOSS WILD-TYPE                         9   103
D57V4, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                           9                103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = 18Q LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED     3   0
  18Q LOSS WILD-TYPE 122   4
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 3                126 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 0                  4 
$`18Q LOSS MUTATED`
TCGA-QT-A5XO TCGA-WB-A819 TCGA-WB-A821 
        2.30         7.69         1.35 

$`18Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
        0.72        25.18         4.41         0.79         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92        97.22        41.06         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 
        2.93         7.10        33.30        23.80         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
       13.32         1.22        11.70        13.05         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02         0.69         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        0.59        20.09        24.00        26.30        23.51        14.50 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       11.38        29.88        29.98        19.76        17.33        10.65 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD 
       11.77         6.08         7.89        12.20       104.55       101.49 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       70.65        67.07        98.07         9.01        99.06         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
        0.10        51.22        54.44        73.05       106.75       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      107.47         3.12        24.66        11.34        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       25.15         7.96        10.42        25.32        14.20        17.16 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF 
        1.18        19.86        12.03        12.49        16.60        17.69 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        10.65        27.62        22.29         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       303.09       127.56        29.16        19.59        32.88 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D 
        5.98        17.46        32.61        26.14        12.20         0.79 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        24.00        24.23        42.54         1.12         1.87 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       19.56        21.44        46.22        12.99        24.82         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 TCGA-XG-A823 
       11.74         9.47        71.05        56.52        92.78         6.90 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              1.35               0.10 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              7.69             303.09 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              2.30              16.88 
[1] "1.4 - 7.7 (2.3)"    "0.1 - 303.1 (16.9)"
[1] "hr="     "3300000"
D58V2, continuous
D58V3, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    2  1
  18Q LOSS WILD-TYPE 71 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2    1
  18Q LOSS WILD-TYPE   71   55
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                2                 71
  MALE                  1                 55
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0     0
  18Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                           1     2
  18Q LOSS WILD-TYPE                         8   110
D58V4, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       1                  8
  WHITE                                           2                110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = 19Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED     4   0
  19Q LOSS WILD-TYPE 121   4
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                125 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 0                  4 
$`19Q LOSS MUTATED`
TCGA-SP-A6QG TCGA-SR-A6MQ TCGA-TT-A6YK TCGA-WB-A81S 
       67.07        54.44        25.15        11.74 

$`19Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       19.86         2.93         7.10        33.30        23.80         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        0.85        13.32         1.22        11.70        13.05         7.96 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 
        6.28        72.79        15.02         0.69         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89         0.59        20.09        24.00        26.30        23.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       14.50        11.38        29.88        29.98        19.76        17.33 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC 
       10.65        11.77         6.08         7.89        12.20       104.55 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
      101.49        70.65        98.07         9.01        99.06         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
        0.10        51.22        73.05       106.75       110.53       107.47 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YN 
        3.12        24.66        11.34        49.61         4.34         7.96 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
       10.42        25.32        14.20        17.16         1.18        19.86 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY 
       12.03        12.49        16.60        17.69        25.61        10.65 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       27.62        22.29         4.47         4.73         4.21       303.09 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 
      127.56        29.16        19.59        32.88         5.98        17.46 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        26.14         7.69        12.20         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T 
       21.44        46.22        12.99        24.82         1.61         9.47 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        56.52         1.35        92.78         6.90 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             11.74               0.10 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             67.07             303.09 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            39.795             14.500 
[1] "11.7 - 67.1 (39.8)" "0.1 - 303.1 (14.5)"
[1] "hr="     "2.6e+07"
D59V2, continuous
D59V3, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    3  1
  19Q LOSS WILD-TYPE 70 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3    1
  19Q LOSS WILD-TYPE   70   55
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                3                 70
  MALE                  1                 55
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     1
  19Q LOSS WILD-TYPE                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           0     3
  19Q LOSS WILD-TYPE                         9   109
D59V4, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                           3                109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = 20Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     3   0
  20Q LOSS WILD-TYPE 122   4
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                126 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 0                  4 
$`20Q LOSS MUTATED`
TCGA-RM-A68W TCGA-W2-A7HC TCGA-W2-A7UY 
        0.92        12.03        10.65 

$`20Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
       38.73        97.22        41.06         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 
        2.93         7.10        33.30        23.80         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
       13.32         1.22        11.70        13.05         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02         0.69         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        0.59        20.09        24.00        26.30        23.51        14.50 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       11.38        29.88        29.98        19.76        17.33        10.65 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD 
       11.77         6.08         7.89        12.20       104.55       101.49 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       70.65        67.07        98.07         9.01        99.06         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
        0.10        51.22        54.44        73.05       106.75       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      107.47         3.12        24.66        11.34        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       25.15         7.96        10.42        25.32        14.20        17.16 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
        1.18        19.86        12.49        16.60        17.69        25.61 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       27.62        22.29         4.47         4.73         4.21       303.09 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 
      127.56        29.16        19.59        32.88         5.98        17.46 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        26.14         7.69        12.20         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       21.44        46.22        12.99        24.82         1.61        11.74 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        9.47        71.05        56.52         1.35        92.78         6.90 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              0.92               0.10 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             12.03             303.09 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             10.65              16.88 
[1] "0.9 - 12.0 (10.7)"  "0.1 - 303.1 (16.9)"
[1] "hr="     "9200000"
D60V2, continuous
D60V3, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    2  1
  20Q LOSS WILD-TYPE 71 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    1
  20Q LOSS WILD-TYPE   71   55
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                2                 71
  MALE                  1                 55
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     0
  20Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           0     3
  20Q LOSS WILD-TYPE                         9   109
D60V4, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  4
  BLACK OR AFRICAN AMERICAN                       0                  9
  WHITE                                           3                109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = 21Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   30  0
  21Q LOSS WILD-TYPE 95  4
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                30                 99 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 0                  4 
$`21Q LOSS MUTATED`
TCGA-PR-A5PF TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RW-A67W 
        7.89         6.94         0.72         2.30         0.79        19.86 
TCGA-RW-A684 TCGA-RW-A68C TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-SP-A6QC TCGA-SP-A6QK 
        1.05         6.28        14.50        11.38       104.55        99.06 
TCGA-SR-A6MP TCGA-SR-A6MT TCGA-SR-A6MV TCGA-SR-A6MZ TCGA-TT-A6YK TCGA-TT-A6YN 
       51.22       106.75       107.47        11.34        25.15         7.96 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-WB-A80L TCGA-WB-A815 
       14.20        17.16         1.18        19.86        22.29         5.98 
TCGA-WB-A816 TCGA-WB-A819 TCGA-WB-A81H TCGA-WB-A81M TCGA-WB-A81S TCGA-WB-A821 
       17.46         7.69        42.54        21.44        11.74         1.35 

$`21Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG 
       31.46        29.03         2.27         0.95         5.88        81.70 
TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A5XN TCGA-QT-A5XP 
       28.01         1.25        36.23         1.81        25.18         4.41 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC 
        0.95        38.73         0.92        97.22        41.06         8.09 
TCGA-RW-A67V TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A685 
       86.89         2.93         7.10        33.30        23.80         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68D 
       13.32         1.22        11.70        13.05         7.96        72.79 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       15.02         0.69         4.41         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WR TCGA-S7-A7WT 
       20.09        24.00        26.30        23.51        29.88        29.98 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 
       19.76        17.33        10.65        11.77         6.08         7.89 
TCGA-S7-A7X2 TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
       12.20       101.49        70.65        67.07        98.07         9.01 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MX 
        1.41         0.10        54.44        73.05       110.53         3.12 
TCGA-SR-A6MY TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HC 
       24.66        49.61         4.34        10.42        25.32        12.03 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       12.49        16.60        17.69        25.61        10.65        27.62 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       303.09       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D 
       19.59        32.88        32.61        26.14        12.20         0.79 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       37.18        24.00        24.23         1.12         1.87        19.56 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V 
       46.22        12.99        24.82         1.61         9.47        71.05 
TCGA-WB-A81W TCGA-WB-A822 TCGA-XG-A823 
       56.52        92.78         6.90 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.72               0.10 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            107.47             303.09 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             12.97              17.33 
[1] "0.7 - 107.5 (13.0)" "0.1 - 303.1 (17.3)"
[1] "hr="     "2.6e+08"
D61V2, continuous
D61V3, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   21  9
  21Q LOSS WILD-TYPE 52 47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     21    9
  21Q LOSS WILD-TYPE   52   47
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               21                 52
  MALE                  9                 47
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  1     1
  21Q LOSS WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                           2    26
  21Q LOSS WILD-TYPE                         7    86
D61V4, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  3
  BLACK OR AFRICAN AMERICAN                       2                  7
  WHITE                                          26                 86
[1] 4 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 = 22Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   44  3
  22Q LOSS WILD-TYPE 81  1
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                47                 82 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                  1 
$`22Q LOSS MUTATED`
TCGA-P8-A5KD TCGA-P8-A6RY TCGA-PR-A5PF TCGA-QT-A5XK TCGA-QT-A5XO TCGA-QT-A5XP 
        2.27         5.88         7.89         6.94         2.30         4.41 
TCGA-QT-A69Q TCGA-RT-A6Y9 TCGA-RW-A67Y TCGA-RW-A681 TCGA-S7-A7WL TCGA-S7-A7WM 
        0.79        97.22         7.10        23.80        20.09        24.00 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SP-A6QF TCGA-SP-A6QG 
       11.38        29.88        11.77        12.20        70.65        67.07 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MX TCGA-SR-A6MZ 
        9.01        99.06         0.10        51.22         3.12        11.34 
TCGA-TT-A6YK TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD 
       25.15        14.20         1.18        19.86        12.03        12.49 
TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7UY TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80V 
       16.60        17.69        10.65         4.73         4.21        29.16 
TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81H TCGA-WB-A81N 
       19.59         5.98         7.69        12.20        42.54        46.22 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81W TCGA-XG-A823 
       24.82         1.61         9.47        56.52         6.90 

$`22Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A6RX TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS 
       31.46        29.03         0.95        81.70        28.01         1.25 
TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A7U0 TCGA-RM-A68T 
       36.23         1.81         0.72        25.18         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
        0.92        41.06         8.09        86.89        19.86         2.93 
TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 
       33.30         1.05         0.85        13.32         1.22        11.70 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G 
       13.05         7.96         6.28        72.79        15.02         0.69 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WO 
        4.41         1.78         2.89         0.59        26.30        23.51 
TCGA-S7-A7WP TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 
       14.50        29.98        19.76        17.33        10.65         6.08 
TCGA-S7-A7X1 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QI TCGA-SQ-A6I4 TCGA-SR-A6MQ 
        7.89       104.55       101.49        98.07         1.41        54.44 
TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MY TCGA-SR-A6N0 
       73.05       106.75       110.53       107.47        24.66        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HH 
        4.34         7.96        10.42        25.32        17.16        25.61 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A814 
       27.62        22.29         4.47       303.09       127.56        32.88 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       17.46        32.61        26.14         0.79        37.18        24.00 
TCGA-WB-A81G TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81P 
       24.23         1.12         1.87        19.56        21.44        12.99 
TCGA-WB-A81S TCGA-WB-A81V TCGA-WB-A821 TCGA-WB-A822 
       11.74        71.05         1.35        92.78 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.10               0.59 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             99.06             303.09 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             12.03              19.66 
[1] "0.1 - 99.1 (12.0)"  "0.6 - 303.1 (19.7)"
[1] "hr=" "6.1"
D62V2, continuous
D62V3, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   28 19
  22Q LOSS WILD-TYPE 45 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     28   19
  22Q LOSS WILD-TYPE   45   37
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               28                 45
  MALE                 19                 37
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  1     2
  22Q LOSS WILD-TYPE                                0     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                           4    40
  22Q LOSS WILD-TYPE                         5    72
D62V4, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  2
  BLACK OR AFRICAN AMERICAN                       4                  5
  WHITE                                          40                 72
[1] 4 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 = XQ LOSS MUTATION ANALYSIS
D63V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   37  1
  XQ LOSS WILD-TYPE 88  3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               38                91 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                 3 
$`XQ LOSS MUTATED`
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RT-A6YA 
       36.23         6.94        25.18         2.30         0.79        41.06 
TCGA-RW-A67Y TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68C TCGA-S7-A7WQ TCGA-S7-A7WR 
        7.10        11.70        13.05         6.28        11.38        29.88 
TCGA-S7-A7WX TCGA-SP-A6QG TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MV TCGA-SR-A6MX 
       11.77        67.07         0.10        54.44       107.47         3.12 
TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
       24.66         4.34         7.96        17.16         1.18        19.86 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HF TCGA-W2-A7UY TCGA-WB-A80M TCGA-WB-A80V 
       12.03        12.49        17.69        10.65         4.47        29.16 
TCGA-WB-A815 TCGA-WB-A819 TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81K TCGA-WB-A81R 
        5.98         7.69        37.18        24.00        19.56         1.61 
TCGA-WB-A81S TCGA-WB-A81W 
       11.74        56.52 

$`XQ LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         2.27         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XP 
       81.70        28.01         1.25         1.81         0.72         4.41 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V 
        0.95        38.73         0.92        97.22         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 
       19.86         2.93        33.30        23.80         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G 
       13.32         1.22         7.96        72.79        15.02         0.69 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89         0.59        20.09        24.00 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       26.30        23.51        14.50        29.98        19.76        17.33 
TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD 
       10.65         6.08         7.89        12.20       104.55       101.49 
TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP 
       70.65        98.07         9.01        99.06         1.41        51.22 
TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YK 
       73.05       106.75       110.53        11.34        49.61        25.15 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HE TCGA-W2-A7HH TCGA-WB-A80K 
       10.42        25.32        14.20        16.60        25.61        27.62 
TCGA-WB-A80L TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80Y 
       22.29         4.73         4.21       303.09       127.56        19.59 
TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D 
       32.88        17.46        32.61        26.14        12.20         0.79 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81M TCGA-WB-A81N 
       24.23        42.54         1.12         1.87        21.44        46.22 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A821 TCGA-WB-A822 
       12.99        24.82         9.47        71.05         1.35        92.78 
TCGA-XG-A823 
        6.90 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.10              0.59 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           107.47            303.09 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            11.90             17.46 
[1] "0.1 - 107.5 (11.9)" "0.6 - 303.1 (17.5)"
[1] "hr=" "1.1"
D63V2, continuous
D63V3, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   23 15
  XQ LOSS WILD-TYPE 50 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     23   15
  XQ LOSS WILD-TYPE   50   41
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              23                50
  MALE                15                41
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  1     1
  XQ LOSS WILD-TYPE                                0     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           5    30
  XQ LOSS WILD-TYPE                         4    82
D63V4, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                 3
  BLACK OR AFRICAN AMERICAN                      5                 4
  WHITE                                         30                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
