[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/15087180/PCPG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PCPG-TP/15096455/transformed.cor.cli.txt"

nPatients in clinical file=179, in cluster file=162, common to both=162
[1] "Reduce the number of clustering variables from 82 to 69."
[1]  69 162
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                7               155 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                7               155 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               19               143 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               19               143 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6               156 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6               156 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               158 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               158 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               159 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               159 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11               151 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11               151 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7               155 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7               155 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               15               147 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               15               147 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8               154 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8               154 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               27               135 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               27               135 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               22               140 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               22               140 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               10               152 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               10               152 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               13               149 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               13               149 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                4               158 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                4               158 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3               159 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3               159 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                150 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                150 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                152 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                152 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                157 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                157 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                11                151 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                11                151 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                14                148 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                14                148 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 9                153 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 9                153 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                158 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                158 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                148 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                148 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                156 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                156 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                156 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                156 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                157 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                157 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 8                154 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 8                154 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                152 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                152 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                20                142 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                20                142 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                14                148 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                14                148 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                150 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                150 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                152 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                152 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                159 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                159 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                159 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                159 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                6               156 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                6               156 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                5               157 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                5               157 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               98                64 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               98                64 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               27               135 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               27               135 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               152 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               152 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               13               149 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               13               149 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               62               100 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               62               100 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               88                74 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               88                74 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               11               151 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               11               151 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10               152 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10               152 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                5               157 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                5               157 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7               155 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7               155 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               19               143 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               19               143 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6               156 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6               156 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               20               142 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               20               142 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               12               150 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               12               150 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               11               151 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               11               151 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11               151 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11               151 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                54                108 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                54                108 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                40                122 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                40                122 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 8                154 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 8                154 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                20                142 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                20                142 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 3                159 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 3                159 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                153 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                153 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                157 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                157 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                61                101 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                61                101 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                19                143 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                19                143 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                16                146 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                16                146 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 6                156 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 6                156 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 6                156 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 6                156 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                159 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                159 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                36                126 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                36                126 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                58                104 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                58                104 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               48               114 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               48               114 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               49               113 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               49               113 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "DCC_UPLOAD_DATE"                       
 [6] "GENDER"                                
 [7] "RADIATION_THERAPY"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[11] "BATCH_NUMBER"                          

Input Data has 11 rows and 162 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=147,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "2"                "128"                 
freq.contrast "128"              "2"                   
both >= 3     "FALSE"            "FALSE"               
Variable 11:'BATCH_NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 162 columns, 1 survival variables, and 3 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH" "GENDER"         "RACE"          
YEARS_TO_BIRTH, nv=57, 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   1
  1P GAIN WILD-TYPE 150   5
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                7               155 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                 5 
$`1P GAIN MUTATED`
TCGA-RW-A681 TCGA-S7-A7WL TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SR-A6MV TCGA-WB-A81J 
       23.80        31.59       114.77       109.25       121.05        24.36 
TCGA-WB-A820 
       10.16 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 
        9.93        14.27        31.53        15.58        32.15         1.28 
TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        4.11       116.19         0.23         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R 
       29.92        13.12         9.01         1.41       117.14        14.20 
TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK 
       41.79         6.02        12.39        17.95        36.23         6.94 
TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q 
        1.81         0.72        25.18         2.30         4.41         0.79 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC 
       13.08        77.98         0.92       108.26        50.63         8.09 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 
       86.89        19.86         2.93         7.10        33.30         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        41.88         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        2.89        20.09        30.21        37.25        35.51        31.04 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       26.96        40.70        37.58        30.51        27.91        20.58 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QF 
       25.32        12.66        18.94        18.08         9.73        82.62 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.50       110.04        15.52       111.25         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MX 
       51.22        68.61        81.93       106.75       110.53         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        19.76        49.61         4.34        25.15        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
       13.32        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 
       34.82        34.26         4.47         4.73         4.21       316.73 
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        41.23 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        34.03        33.90        24.16        35.84        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M 
       57.11        38.76        42.54        22.32        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       53.69        12.99        24.82         1.61        23.77        18.28 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        78.21        93.11       103.17        20.19 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            10.16              0.10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           121.05            316.73 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            31.59             20.09 
[1] "10.2 - 121.0 (31.6)" "0.1 - 316.7 (20.1)" 
[1] "hr=" "2.4"
D1V2, continuous
D1V3, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    1  6
  1P GAIN WILD-TYPE 87 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    6
  1P GAIN WILD-TYPE   87   68
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               1                87
  MALE                 6                68
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     0
  1P GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           0     6
  1P GAIN WILD-TYPE                        19   128
D1V4, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          6               128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    17   2
  1Q GAIN WILD-TYPE 139   4
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               19               143 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                2                 4 
$`1Q GAIN MUTATED`
TCGA-P7-A5NY TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A70R TCGA-RW-A680 TCGA-RW-A681 
       31.46       137.59        19.04        14.20        33.30        23.80 
TCGA-S7-A7WL TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SR-A6MV TCGA-SR-A6MZ TCGA-WB-A80P 
       31.59       114.77       109.25       121.05        19.76       316.73 
TCGA-WB-A815 TCGA-WB-A819 TCGA-WB-A81G TCGA-WB-A81J TCGA-WB-A81Q TCGA-WB-A81W 
        5.98        33.90        38.76        24.36        24.82        78.21 
TCGA-WB-A820 
       10.16 

$`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        17.75         5.88        17.95        81.70 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GU TCGA-QR-A6GY 
       28.08        35.01        23.11         1.25        58.88         1.05 
TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
       30.51         9.21        14.17         9.93        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D 
       15.58        32.15         1.28         4.11       116.19         0.23 
TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K 
        6.31         2.33        26.83        29.92        13.12         9.01 
TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
        1.41       117.14        41.79         6.02        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       36.23         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        4.41         0.79        13.08        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       50.63         8.09        86.89        19.86         2.93         7.10 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
        1.05         0.85        13.32         1.22        11.70        13.05 
TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
        7.96         6.28        72.79        15.02        41.88         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        1.78         2.89        20.09        30.21        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       31.04        26.96        40.70        37.58        30.51        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 
       20.58        25.32        12.66        18.94        18.08         9.73 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       82.62        67.50       110.04        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
        0.10        51.22        68.61        81.93       106.75       110.53 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
        3.12        24.66        49.61         4.34        25.15        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
       13.32        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-A80Q 
       34.82        34.26         4.47         4.73         4.21       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 
       29.16        19.59        32.88        41.23        32.61        34.03 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81H TCGA-WB-A81I 
       24.16        35.84        37.18        57.11        42.54        22.32 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S 
       40.04        45.83        53.69        12.99         1.61        23.77 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       18.28        71.05        93.11       103.17        20.19 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             5.98              0.10 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           316.73            127.56 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            31.59             19.86 
[1] "6.0 - 316.7 (31.6)" "0.1 - 127.6 (19.9)"
[1] "hr=" "1.9"
D2V2, continuous
D2V3, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    7 12
  1Q GAIN WILD-TYPE 81 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      7   12
  1Q GAIN WILD-TYPE   81   62
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               7                81
  MALE                12                62
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  0     0
  1Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                           1    17
  1Q GAIN WILD-TYPE                        18   117
D2V4, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         17               117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED     6   0
  2P GAIN WILD-TYPE 150   6
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6               156 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                0                 6 
$`2P GAIN MUTATED`
TCGA-QR-A6GZ TCGA-QR-A700 TCGA-QR-A7IP TCGA-RW-A68D TCGA-RW-A68F TCGA-WB-A81D 
       30.51        32.15        17.95        72.79        15.02        35.84 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       58.88        19.04         1.05         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       14.27        31.53        15.58         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
        9.01         1.41       117.14        14.20        41.79         6.02 
TCGA-QR-A7IN TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
       12.39        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        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
      108.26        50.63         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-A68G 
        1.22        11.70        13.05         7.96         6.28        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89        20.09        31.59        30.21 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       37.25        35.51        31.04        26.96        40.70        37.58 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 
       30.51        27.91        20.58        25.32        12.66        18.94 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       18.08         9.73       114.77       109.25        82.62        67.50 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
      110.04        15.52       111.25         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX 
       68.61        81.93       106.75       110.53       121.05         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        19.76        49.61         4.34        25.15        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
       13.32        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 
       34.82        34.26         4.47         4.73         4.21       316.73 
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        41.23 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81E TCGA-WB-A81F 
       32.61        34.03        33.90        24.16        37.18        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        42.54        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       53.69        12.99        24.82         1.61        23.77        18.28 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        78.21        10.16        93.11       103.17        20.19 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            15.02              0.10 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            72.79            316.73 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           31.330            20.385 
[1] "15.0 - 72.8 (31.3)" "0.1 - 316.7 (20.4)"
[1] "hr="     "2.6e+07"
D3V2, continuous
D3V3, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    3  3
  2P GAIN WILD-TYPE 85 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3    3
  2P GAIN WILD-TYPE   85   71
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               3                85
  MALE                 3                71
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  0     1
  2P GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                           0     5
  2P GAIN WILD-TYPE                        19   129
D3V4, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          5               129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = 4P GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     4   0
  4P GAIN WILD-TYPE 152   6
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               158 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                0                 6 
$`4P GAIN MUTATED`
TCGA-QR-A6GZ TCGA-RW-A68D TCGA-SP-A6QI TCGA-WB-A80K 
       30.51        72.79       110.04        34.82 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       58.88        19.04         1.05         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 
       14.27        31.53        15.58        32.15         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
      116.19         0.23         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W 
       13.12         9.01         1.41       117.14        14.20        41.79 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
        6.02        12.39        17.95        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        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       77.98         0.92       108.26        50.63         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        41.88         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        30.21        37.25        35.51        31.04 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       26.96        40.70        37.58        30.51        27.91        20.58 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       25.32        12.66        18.94        18.08         9.73       114.77 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
      109.25        82.62        67.50        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
        0.10        51.22        68.61        81.93       106.75       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      121.05         3.12        24.66        19.76        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       25.15        19.92        13.32        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-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       25.61        10.65        34.26         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      316.73       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 
       41.23        32.61        34.03        33.90        24.16        35.84 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        57.11        38.76        42.54        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       40.04        45.83        53.69        12.99        24.82         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 
       23.77        18.28        71.05        78.21        10.16        93.11 
TCGA-WB-A822 TCGA-XG-A823 
      103.17        20.19 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            30.51              0.10 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           110.04            316.73 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           53.805            20.140 
[1] "30.5 - 110.0 (53.8)" "0.1 - 316.7 (20.1)" 
[1] "hr="     "2.6e+07"
D4V2, continuous
D4V3, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    1  3
  4P GAIN WILD-TYPE 87 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    3
  4P GAIN WILD-TYPE   87   71
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               1                87
  MALE                 3                71
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     1
  4P GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           0     3
  4P GAIN WILD-TYPE                        19   131
D4V4, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = 4Q GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     3   0
  4Q GAIN WILD-TYPE 153   6
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               159 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                0                 6 
$`4Q GAIN MUTATED`
TCGA-RW-A688 TCGA-SP-A6QI TCGA-WB-A80K 
        1.22       110.04        34.82 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 
        9.93        14.27        31.53        15.58        32.15         1.28 
TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        4.11       116.19         0.23         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R 
       29.92        13.12         9.01         1.41       117.14        14.20 
TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK 
       41.79         6.02        12.39        17.95        36.23         6.94 
TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q 
        1.81         0.72        25.18         2.30         4.41         0.79 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC 
       13.08        77.98         0.92       108.26        50.63         8.09 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 
       86.89        19.86         2.93         7.10        33.30        23.80 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        1.05         0.85        13.32        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        41.88         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89        20.09        31.59        30.21        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       31.04        26.96        40.70        37.58        30.51        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 
       20.58        25.32        12.66        18.94        18.08         9.73 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QJ TCGA-SP-A6QK 
      114.77       109.25        82.62        67.50        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT 
        1.41         0.10        51.22        68.61        81.93       106.75 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
      110.53       121.05         3.12        24.66        19.76        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        25.15        19.92        13.32        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-A80L TCGA-WB-A80M TCGA-WB-A80N 
       17.69        25.61        10.65        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       316.73       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        41.23        32.61        34.03        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       24.36        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
        1.61        23.77        18.28        71.05        78.21        10.16 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       93.11       103.17        20.19 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             1.22              0.10 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           110.04            316.73 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            34.82             20.58 
[1] "1.2 - 110.0 (34.8)" "0.1 - 316.7 (20.6)"
[1] "hr="     "9200000"
D5V2, continuous
D5V3, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    1  2
  4Q GAIN WILD-TYPE 87 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    2
  4Q GAIN WILD-TYPE   87   72
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               1                87
  MALE                 2                72
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     0
  4Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           0     3
  4Q GAIN WILD-TYPE                        19   131
D5V4, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      0                19
  WHITE                                          3               131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = 5P GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    11   0
  5P GAIN WILD-TYPE 145   6
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11               151 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                0                 6 
$`5P GAIN MUTATED`
TCGA-QR-A6GX TCGA-QR-A70K TCGA-S7-A7WL TCGA-SR-A6MT TCGA-SR-A6N0 TCGA-W2-A7H5 
       19.04         9.01        31.59       106.75        49.61        14.20 
TCGA-WB-A80K TCGA-WB-A815 TCGA-WB-A81A TCGA-WB-A81T TCGA-WB-A821 
       34.82         5.98        24.16        18.28        93.11 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       58.88         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 
       14.27        31.53        15.58        32.15         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
      116.19         0.23         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
       13.12         1.41       117.14        14.20        41.79         6.02 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       12.39        17.95        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        13.08        77.98 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92       108.26        50.63         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        41.88         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       20.09        30.21        37.25        35.51        31.04        26.96 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       40.70        37.58        30.51        27.91        20.58        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       12.66        18.94        18.08         9.73       114.77       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       82.62        67.50       110.04        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV 
        0.10        51.22        68.61        81.93       110.53       121.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
        3.12        24.66        19.76         4.34        25.15        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC 
       13.32        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        34.26 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       316.73       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        41.23        32.61        34.03        33.90 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       24.36        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A822 
        1.61        23.77        71.05        78.21        10.16       103.17 
TCGA-XG-A823 
       20.19 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             5.98              0.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           106.75            316.73 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            24.16             20.58 
[1] "6.0 - 106.8 (24.2)" "0.1 - 316.7 (20.6)"
[1] "hr="     "7.4e+07"
D6V2, continuous
D6V3, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    7  4
  5P GAIN WILD-TYPE 81 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7    4
  5P GAIN WILD-TYPE   81   70
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               7                81
  MALE                 4                70
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  0     0
  5P GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                           1    10
  5P GAIN WILD-TYPE                        18   124
D6V4, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         10               124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = 5Q GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED     7   0
  5Q GAIN WILD-TYPE 149   6
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7               155 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                0                 6 
$`5Q GAIN MUTATED`
TCGA-QR-A6GX TCGA-SR-A6MT TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-W2-A7H5 TCGA-WB-A80K 
       19.04       106.75        19.76        49.61        14.20        34.82 
TCGA-WB-A821 
       93.11 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       58.88         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 
       14.27        31.53        15.58        32.15         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
      116.19         0.23         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W 
       13.12         9.01         1.41       117.14        14.20        41.79 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
        6.02        12.39        17.95        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        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       77.98         0.92       108.26        50.63         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        41.88         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89        20.09        31.59        30.21        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       31.04        26.96        40.70        37.58        30.51        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 
       20.58        25.32        12.66        18.94        18.08         9.73 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      114.77       109.25        82.62        67.50       110.04        15.52 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
      111.25         1.41         0.10        51.22        68.61        81.93 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-TT-A6YK 
      110.53       121.05         3.12        24.66         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
       19.92        13.32        25.32        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-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       34.26         4.47         4.73         4.21       316.73       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        41.23        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       34.03        33.90        24.16        35.84        37.18        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        42.54        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       53.69        12.99        24.82         1.61        23.77        18.28 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A822 TCGA-XG-A823 
       71.05        78.21        10.16       103.17        20.19 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             14.2               0.1 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           106.75            316.73 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            34.82             20.58 
[1] "14.2 - 106.8 (34.8)" "0.1 - 316.7 (20.6)" 
[1] "hr="     "2.6e+07"
D7V2, continuous
D7V3, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    6  1
  5Q GAIN WILD-TYPE 82 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      6    1
  5Q GAIN WILD-TYPE   82   73
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               6                82
  MALE                 1                73
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     0
  5Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           1     6
  5Q GAIN WILD-TYPE                        18   128
D7V4, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          6               128
[1] 4 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    15   0
  6P GAIN WILD-TYPE 141   6
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               15               147 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                0                 6 
$`6P GAIN MUTATED`
TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QR-A6GX TCGA-QR-A6GZ TCGA-QR-A700 
        2.27        81.70        35.01        19.04        30.51        32.15 
TCGA-QR-A70N TCGA-RM-A68W TCGA-RW-A684 TCGA-S7-A7WN TCGA-S7-A7X1 TCGA-W2-A7H5 
        1.41         0.92         1.05        37.25        18.94        14.20 
TCGA-WB-A80L TCGA-WB-A819 TCGA-WB-A821 
       34.26        33.90        93.11 

$`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        17.75         5.88        17.95        28.08 
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6H0 
       23.11         1.25       137.59        58.88         1.05         9.21 
TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 
       14.17         9.93        14.27        31.53        15.58         1.28 
TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        4.11       116.19         0.23         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W 
       29.92        13.12         9.01       117.14        14.20        41.79 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
        6.02        12.39        17.95        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        13.08 
TCGA-RM-A68T TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
       77.98       108.26        50.63         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A685 TCGA-RW-A686 
        2.93         7.10        33.30        23.80         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        41.88         4.41         1.78         2.89        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       31.59        30.21        35.51        31.04        26.96        40.70 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       37.58        30.51        27.91        20.58        25.32        12.66 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       18.08         9.73       114.77       109.25        82.62        67.50 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
      110.04        15.52       111.25         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX 
       68.61        81.93       106.75       110.53       121.05         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        19.76        49.61         4.34        25.15        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC 
       13.32        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        34.82 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       316.73       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        41.23        32.61        34.03 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       24.16        35.84        37.18        57.11        38.76        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       22.32        24.36        40.04        45.83        53.69        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        23.77        18.28        71.05        78.21 
TCGA-WB-A820 TCGA-WB-A822 TCGA-XG-A823 
       10.16       103.17        20.19 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.92              0.10 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            93.11            316.73 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            30.51             20.58 
[1] "0.9 - 93.1 (30.5)"  "0.1 - 316.7 (20.6)"
[1] "hr="     "7.6e+07"
D8V2, continuous
D8V3, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    8  7
  6P GAIN WILD-TYPE 80 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      8    7
  6P GAIN WILD-TYPE   80   67
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               8                80
  MALE                 7                67
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0     0
  6P GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           2    13
  6P GAIN WILD-TYPE                        17   121
D8V4, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                         13               121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = 6Q GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED     8   0
  6Q GAIN WILD-TYPE 148   6
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8               154 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                0                 6 
$`6Q GAIN MUTATED`
TCGA-QR-A6GX TCGA-QR-A6GZ TCGA-QR-A700 TCGA-QR-A70N TCGA-S7-A7X1 TCGA-W2-A7H5 
       19.04        30.51        32.15         1.41        18.94        14.20 
TCGA-WB-A80L TCGA-WB-A821 
       34.26        93.11 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
       58.88         1.05         9.21        14.17         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D 
       31.53        15.58         1.28         4.11       116.19         0.23 
TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K 
        6.31         2.33        26.83        29.92        13.12         9.01 
TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
      117.14        14.20        41.79         6.02        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       36.23         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        4.41         0.79        13.08        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       50.63         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 
       41.88         4.41         1.78         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       30.21        37.25        35.51        31.04        26.96        40.70 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       37.58        30.51        27.91        20.58        25.32        12.66 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       18.08         9.73       114.77       109.25        82.62        67.50 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
      110.04        15.52       111.25         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX 
       68.61        81.93       106.75       110.53       121.05         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        19.76        49.61         4.34        25.15        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC 
       13.32        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        34.82 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       316.73       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        41.23        32.61        34.03 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
       33.90        24.16        35.84        37.18        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54        22.32        24.36        40.04        45.83        53.69 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       12.99        24.82         1.61        23.77        18.28        71.05 
TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A822 TCGA-XG-A823 
       78.21        10.16       103.17        20.19 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             1.41              0.10 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            93.11            316.73 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           24.775            21.450 
[1] "1.4 - 93.1 (24.8)"  "0.1 - 316.7 (21.4)"
[1] "hr="     "2.6e+07"
D9V2, continuous
D9V3, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    4  4
  6Q GAIN WILD-TYPE 84 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      4    4
  6Q GAIN WILD-TYPE   84   70
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               4                84
  MALE                 4                70
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     0
  6Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           2     6
  6Q GAIN WILD-TYPE                        17   128
D9V4, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          6               128
[1] 4 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    27   0
  7P GAIN WILD-TYPE 129   6
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               27               135 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                0                 6 
$`7P GAIN MUTATED`
TCGA-P8-A6RX TCGA-PR-A5PG TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A700 
       17.75        81.70        19.04         1.05        30.51        32.15 
TCGA-QR-A70N TCGA-QT-A5XM TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RT-A6YC TCGA-RW-A681 
        1.41         0.72         0.79        13.08         8.09        23.80 
TCGA-RW-A684 TCGA-RW-A68G TCGA-S7-A7WL TCGA-S7-A7WW TCGA-S7-A7X1 TCGA-SR-A6MT 
        1.05        41.88        31.59        20.58        18.94       106.75 
TCGA-SR-A6MU TCGA-SR-A6N0 TCGA-W2-A7H7 TCGA-WB-A80L TCGA-WB-A80O TCGA-WB-A815 
      110.53        49.61        17.16        34.26         4.21         5.98 
TCGA-WB-A81A TCGA-WB-A81N TCGA-WB-A821 
       24.16        53.69        93.11 

$`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        17.95        28.08 
TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6H0 
       35.01        23.11         1.25       137.59        58.88         9.21 
TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 
       14.17         9.93        14.27        31.53        15.58         1.28 
TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        4.11       116.19         0.23         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W 
       29.92        13.12         9.01       117.14        14.20        41.79 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
        6.02        12.39        17.95        36.23         6.94         1.81 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
       25.18         2.30         4.41        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 
       50.63        86.89        19.86         2.93         7.10        33.30 
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-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
        6.28        72.79        15.02         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       20.09        30.21        37.25        35.51        31.04        26.96 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X0 
       40.70        37.58        30.51        27.91        25.32        12.66 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       18.08         9.73       114.77       109.25        82.62        67.50 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
      110.04        15.52       111.25         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
       68.61        81.93       121.05         3.12        24.66        19.76 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        25.15        19.92        13.32        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-A80M TCGA-WB-A80N TCGA-WB-A80P 
       25.61        10.65        34.82         4.47         4.73       316.73 
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        41.23        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
       34.03        33.90        35.84        37.18        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81P 
       42.54        22.32        24.36        40.04        45.83        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        23.77        18.28        71.05        78.21 
TCGA-WB-A820 TCGA-WB-A822 TCGA-XG-A823 
       10.16       103.17        20.19 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.72              0.10 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           110.53            316.73 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            20.58             22.32 
[1] "0.7 - 110.5 (20.6)" "0.1 - 316.7 (22.3)"
[1] "hr="     "8.6e+07"
D10V2, continuous
D10V3, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   13 14
  7P GAIN WILD-TYPE 75 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     13   14
  7P GAIN WILD-TYPE   75   60
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              13                75
  MALE                14                60
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  0     0
  7P GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                           2    25
  7P GAIN WILD-TYPE                        17   109
D10V4, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                         25               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(11) Variable = 7Q GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    22   0
  7Q GAIN WILD-TYPE 134   6
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               22               140 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                0                 6 
$`7Q GAIN MUTATED`
TCGA-P8-A6RX TCGA-QR-A6GX TCGA-QR-A6GZ TCGA-QR-A700 TCGA-QR-A70N TCGA-QT-A5XM 
       17.75        19.04        30.51        32.15         1.41         0.72 
TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RT-A6YC TCGA-RW-A681 TCGA-RW-A684 TCGA-RX-A8JQ 
        0.79        13.08         8.09        23.80         1.05        20.09 
TCGA-S7-A7WL TCGA-S7-A7WW TCGA-S7-A7X1 TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6N0 
       31.59        20.58        18.94       106.75       110.53        49.61 
TCGA-W2-A7H7 TCGA-WB-A80L TCGA-WB-A81A TCGA-WB-A821 
       17.16        34.26        24.16        93.11 

$`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        17.95        81.70 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU 
       28.08        35.01        23.11         1.25       137.59        58.88 
TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
        1.05         9.21        14.17         9.93        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E 
       15.58         1.28         4.11       116.19         0.23         6.31 
TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70P 
        2.33        26.83        29.92        13.12         9.01       117.14 
TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ 
       14.20        41.79         6.02        12.39        17.95        36.23 
TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-RM-A68T 
        6.94         1.81        25.18         2.30         4.41        77.98 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
        0.92       108.26        50.63        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 
        7.10        33.30         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        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        4.41         1.78         2.89        30.21        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       31.04        26.96        40.70        37.58        30.51        27.91 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       25.32        12.66        18.08         9.73       114.77       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       82.62        67.50       110.04        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MV TCGA-SR-A6MX 
        0.10        51.22        68.61        81.93       121.05         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       24.66        19.76         4.34        25.15        19.92        13.32 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD 
       25.32        14.20         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        34.82         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       316.73       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        41.23        32.61        34.03        33.90 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       24.36        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
        1.61        23.77        18.28        71.05        78.21        10.16 
TCGA-WB-A822 TCGA-XG-A823 
      103.17        20.19 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.72              0.10 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           110.53            316.73 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           20.335            22.715 
[1] "0.7 - 110.5 (20.3)" "0.1 - 316.7 (22.7)"
[1] "hr="     "8.2e+07"
D11V2, continuous
D11V3, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    8 14
  7Q GAIN WILD-TYPE 80 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      8   14
  7Q GAIN WILD-TYPE   80   60
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               8                80
  MALE                14                60
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  0     0
  7Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                           2    20
  7Q GAIN WILD-TYPE                        17   114
D11V4, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                         20               114
[1] 4 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    10   0
  8P GAIN WILD-TYPE 146   6
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               10               152 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                0                 6 
$`8P GAIN MUTATED`
TCGA-QR-A6GZ TCGA-QR-A70N TCGA-QR-A70R TCGA-QT-A5XN TCGA-RM-A68W TCGA-RW-A681 
       30.51         1.41        14.20        25.18         0.92        23.80 
TCGA-S7-A7WW TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6N0 
       20.58        81.93       110.53        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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       58.88        19.04         1.05         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 
       14.27        31.53        15.58        32.15         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
      116.19         0.23         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
       13.12         9.01       117.14        41.79         6.02        12.39 
TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XO 
       17.95        36.23         6.94         1.81         0.72         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RT-A6Y9 TCGA-RT-A6YA 
        4.41         0.79        13.08        77.98       108.26        50.63 
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-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
        1.05         0.85        13.32         1.22        11.70        13.05 
TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
        7.96         6.28        72.79        15.02        41.88         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89        20.09        31.59        30.21        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       35.51        31.04        26.96        40.70        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 
       27.91        25.32        12.66        18.94        18.08         9.73 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      114.77       109.25        82.62        67.50       110.04        15.52 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MT 
      111.25         1.41         0.10        51.22        68.61       106.75 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK 
      121.05         3.12        24.66        19.76         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       19.92        13.32        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        34.82        34.26         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      316.73       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 
       41.23        32.61        34.03        33.90        24.16        35.84 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        57.11        38.76        42.54        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       40.04        45.83        53.69        12.99        24.82         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 
       23.77        18.28        71.05        78.21        10.16        93.11 
TCGA-WB-A822 TCGA-XG-A823 
      103.17        20.19 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.92              0.10 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           110.53            316.73 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            24.49             20.14 
[1] "0.9 - 110.5 (24.5)" "0.1 - 316.7 (20.1)"
[1] "hr="     "2.7e+07"
D12V2, continuous
D12V3, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    5  5
  8P GAIN WILD-TYPE 83 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    5
  8P GAIN WILD-TYPE   83   69
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               5                83
  MALE                 5                69
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     0
  8P GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           2     8
  8P GAIN WILD-TYPE                        17   126
D12V4, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          8               126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = 8Q GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    12   1
  8Q GAIN WILD-TYPE 144   5
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               13               149 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                1                 5 
$`8Q GAIN MUTATED`
TCGA-QR-A6GZ TCGA-QR-A70N TCGA-QR-A70R TCGA-QT-A5XN TCGA-RM-A68W TCGA-RW-A681 
       30.51         1.41        14.20        25.18         0.92        23.80 
TCGA-RW-A8AZ TCGA-S7-A7WW TCGA-SP-A6QF TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6N0 
        2.89        20.58        82.62        81.93       110.53        49.61 
TCGA-W2-A7HE 
       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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       58.88        19.04         1.05         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 
       14.27        31.53        15.58        32.15         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
      116.19         0.23         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
       13.12         9.01       117.14        41.79         6.02        12.39 
TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XO 
       17.95        36.23         6.94         1.81         0.72         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RT-A6Y9 TCGA-RT-A6YA 
        4.41         0.79        13.08        77.98       108.26        50.63 
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-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
        1.05         0.85        13.32         1.22        11.70        13.05 
TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
        7.96         6.28        72.79        15.02        41.88         4.41 
TCGA-RW-A7D0 TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        1.78        20.09        31.59        30.21        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       31.04        26.96        40.70        37.58        30.51        27.91 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       25.32        12.66        18.94        18.08         9.73       114.77 
TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
      109.25        67.50       110.04        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MT TCGA-SR-A6MV TCGA-SR-A6MX 
        0.10        51.22        68.61       106.75       121.05         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       24.66        19.76         4.34        25.15        19.92        13.32 
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-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L 
       12.49        17.69        25.61        10.65        34.82        34.26 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       316.73       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        41.23        32.61        34.03 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
       33.90        24.16        35.84        37.18        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54        22.32        24.36        40.04        45.83        53.69 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       12.99        24.82         1.61        23.77        18.28        71.05 
TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       78.21        10.16        93.11       103.17        20.19 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.92              0.10 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           110.53            316.73 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            23.80             20.19 
[1] "0.9 - 110.5 (23.8)" "0.1 - 316.7 (20.2)"
[1] "hr=" "2.8"
D13V2, continuous
D13V3, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    5  8
  8Q GAIN WILD-TYPE 83 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5    8
  8Q GAIN WILD-TYPE   83   66
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               5                83
  MALE                 8                66
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     1
  8Q GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                           2    10
  8Q GAIN WILD-TYPE                        17   124
D13V4, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                         10               124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = 9P GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     4   0
  9P GAIN WILD-TYPE 152   6
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                4               158 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                 6 
$`9P GAIN MUTATED`
TCGA-QR-A70N TCGA-SR-A6MT TCGA-W2-A7H7 TCGA-WB-A80L 
        1.41       106.75        17.16        34.26 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 
        9.93        14.27        31.53        15.58        32.15         1.28 
TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        4.11       116.19         0.23         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W 
       29.92        13.12         9.01       117.14        14.20        41.79 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
        6.02        12.39        17.95        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        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       77.98         0.92       108.26        50.63         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        41.88         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89        20.09        31.59        30.21        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       31.04        26.96        40.70        37.58        30.51        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 
       20.58        25.32        12.66        18.94        18.08         9.73 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      114.77       109.25        82.62        67.50       110.04        15.52 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
      111.25         1.41         0.10        51.22        68.61        81.93 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
      110.53       121.05         3.12        24.66        19.76        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        25.15        19.92        13.32        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-A80M TCGA-WB-A80N TCGA-WB-A80O 
       25.61        10.65        34.82         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      316.73       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 
       41.23        32.61        34.03        33.90        24.16        35.84 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        57.11        38.76        42.54        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       40.04        45.83        53.69        12.99        24.82         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 
       23.77        18.28        71.05        78.21        10.16        93.11 
TCGA-WB-A822 TCGA-XG-A823 
      103.17        20.19 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.41              0.10 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           106.75            316.73 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            25.71             21.45 
[1] "1.4 - 106.8 (25.7)" "0.1 - 316.7 (21.4)"
[1] "hr="     "9200000"
D14V2, continuous
D14V3, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    2  2
  9P GAIN WILD-TYPE 86 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    2
  9P GAIN WILD-TYPE   86   72
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               2                86
  MALE                 2                72
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     0
  9P GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           1     3
  9P GAIN WILD-TYPE                        18   131
D14V4, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          3               131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = 9Q GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     3   0
  9Q GAIN WILD-TYPE 153   6
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3               159 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                0                 6 
$`9Q GAIN MUTATED`
TCGA-QR-A70N TCGA-SR-A6MT TCGA-WB-A80L 
        1.41       106.75        34.26 

$`9Q 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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 
        9.93        14.27        31.53        15.58        32.15         1.28 
TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        4.11       116.19         0.23         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W 
       29.92        13.12         9.01       117.14        14.20        41.79 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
        6.02        12.39        17.95        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        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       77.98         0.92       108.26        50.63         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        41.88         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89        20.09        31.59        30.21        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       31.04        26.96        40.70        37.58        30.51        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 
       20.58        25.32        12.66        18.94        18.08         9.73 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      114.77       109.25        82.62        67.50       110.04        15.52 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
      111.25         1.41         0.10        51.22        68.61        81.93 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
      110.53       121.05         3.12        24.66        19.76        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        25.15        19.92        13.32        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-A80N 
       17.69        25.61        10.65        34.82         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       316.73       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        41.23        32.61        34.03        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       24.36        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
        1.61        23.77        18.28        71.05        78.21        10.16 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       93.11       103.17        20.19 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1.41              0.10 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           106.75            316.73 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            34.26             20.58 
[1] "1.4 - 106.8 (34.3)" "0.1 - 316.7 (20.6)"
[1] "hr="     "9200000"
D15V2, continuous
D15V3, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    2  1
  9Q GAIN WILD-TYPE 86 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    1
  9Q GAIN WILD-TYPE   86   73
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               2                86
  MALE                 1                73
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     0
  9Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                           1     2
  9Q GAIN WILD-TYPE                        18   132
D15V4, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          2               132
[1] 4 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 = 10P GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    12   0
  10P GAIN WILD-TYPE 144   6
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                150 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 0                  6 
$`10P GAIN MUTATED`
TCGA-QR-A6GX TCGA-QR-A6H1 TCGA-QR-A70N TCGA-RW-A681 TCGA-RW-A688 TCGA-RW-A68B 
       19.04        14.17         1.41        23.80         1.22         7.96 
TCGA-SR-A6MT TCGA-SR-A6MZ TCGA-W2-A7H5 TCGA-W2-A7HE TCGA-WB-A80L TCGA-WB-A81A 
      106.75        19.76        14.20        16.60        34.26        24.16 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 
       58.88         1.05        30.51         9.21         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       31.53        15.58        32.15         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
        9.01       117.14        14.20        41.79         6.02        12.39 
TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
       17.95        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        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
      108.26        50.63         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-A689 
        7.10        33.30         1.05         0.85        13.32        11.70 
TCGA-RW-A68A TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
       13.05         6.28        72.79        15.02        41.88         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89        20.09        31.59        30.21        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       35.51        31.04        26.96        40.70        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       27.91        20.58        25.32        12.66        18.94        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
        9.73       114.77       109.25        82.62        67.50       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       15.52       111.25         1.41         0.10        51.22        68.61 
TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6N0 
       81.93       110.53       121.05         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        19.92        13.32        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-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       10.65        34.82         4.47         4.73         4.21       316.73 
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        41.23 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       32.61        34.03        33.90        35.84        37.18        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        42.54        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       53.69        12.99        24.82         1.61        23.77        18.28 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        78.21        10.16        93.11       103.17        20.19 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1.22               0.10 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            106.75             316.73 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             17.82              23.44 
[1] "1.2 - 106.8 (17.8)" "0.1 - 316.7 (23.4)"
[1] "hr="     "2.7e+07"
D16V2, continuous
D16V3, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    7  5
  10P GAIN WILD-TYPE 81 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      7    5
  10P GAIN WILD-TYPE   81   69
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                7                 81
  MALE                  5                 69
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0     0
  10P GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           2     9
  10P GAIN WILD-TYPE                        17   125
D16V4, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       2                 17
  WHITE                                           9                125
[1] 4 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 = 10Q GAIN MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    10   0
  10Q GAIN WILD-TYPE 146   6
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                152 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 0                  6 
$`10Q GAIN MUTATED`
TCGA-QR-A6H1 TCGA-QR-A70N TCGA-RW-A681 TCGA-RW-A688 TCGA-RW-A68B TCGA-SP-A6QC 
       14.17         1.41        23.80         1.22         7.96       114.77 
TCGA-SR-A6MT TCGA-SR-A6MZ TCGA-W2-A7H5 TCGA-W2-A7HE 
      106.75        19.76        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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H2 
       58.88        19.04         1.05        30.51         9.21         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 
       14.27        31.53        15.58        32.15         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
      116.19         0.23         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
       13.12         9.01       117.14        14.20        41.79         6.02 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       12.39        17.95        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        13.08        77.98 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92       108.26        50.63         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-A689 TCGA-RW-A68A TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G 
       11.70        13.05         6.28        72.79        15.02        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89        20.09        31.59        30.21 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       37.25        35.51        31.04        26.96        40.70        37.58 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 
       30.51        27.91        20.58        25.32        12.66        18.94 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
       18.08         9.73       109.25        82.62        67.50       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       15.52       111.25         1.41         0.10        51.22        68.61 
TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6N0 
       81.93       110.53       121.05         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        19.92        13.32        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        34.82        34.26         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      316.73       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 
       41.23        32.61        34.03        33.90        24.16        35.84 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        57.11        38.76        42.54        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       40.04        45.83        53.69        12.99        24.82         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 
       23.77        18.28        71.05        78.21        10.16        93.11 
TCGA-WB-A822 TCGA-XG-A823 
      103.17        20.19 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1.22               0.10 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            114.77             316.73 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             15.40              23.44 
[1] "1.2 - 114.8 (15.4)" "0.1 - 316.7 (23.4)"
[1] "hr="     "2.6e+07"
D17V2, continuous
D17V3, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    4  6
  10Q GAIN WILD-TYPE 84 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      4    6
  10Q GAIN WILD-TYPE   84   68
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                4                 84
  MALE                  6                 68
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     0
  10Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           1     8
  10Q GAIN WILD-TYPE                        18   126
D17V4, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           8                126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = 11P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     5   0
  11P GAIN WILD-TYPE 151   6
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                157 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                  6 
$`11P GAIN MUTATED`
TCGA-P8-A5KD TCGA-PR-A5PF TCGA-RW-A689 TCGA-W2-A7H5 TCGA-WB-A80O 
        2.27        17.95        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        17.75         5.88        81.70        28.08 
TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GX 
       35.01        23.11         1.25       137.59        58.88        19.04 
TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
        1.05        30.51         9.21        14.17         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       31.53        15.58        32.15         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
        9.01         1.41       117.14        14.20        41.79         6.02 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       12.39        17.95        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        13.08        77.98 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92       108.26        50.63         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-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D 
       13.32         1.22        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        41.88         4.41         1.78         2.89        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       31.59        30.21        37.25        35.51        31.04        26.96 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       40.70        37.58        30.51        27.91        20.58        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       12.66        18.94        18.08         9.73       114.77       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       82.62        67.50       110.04        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
        0.10        51.22        68.61        81.93       106.75       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      121.05         3.12        24.66        19.76        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA 
       25.15        19.92        13.32        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-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80P 
       10.65        34.82        34.26         4.47         4.73       316.73 
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        41.23 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        34.03        33.90        24.16        35.84        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       57.11        38.76        42.54        22.32        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       45.83        53.69        12.99        24.82         1.61        23.77 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 
       18.28        71.05        78.21        10.16        93.11       103.17 
TCGA-XG-A823 
       20.19 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              2.27               0.10 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             17.95             316.73 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             11.70              23.77 
[1] "2.3 - 17.9 (11.7)"  "0.1 - 316.7 (23.8)"
[1] "hr="     "9300000"
D18V2, continuous
D18V3, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    4  1
  11P GAIN WILD-TYPE 84 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      4    1
  11P GAIN WILD-TYPE   84   73
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                4                 84
  MALE                  1                 73
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     0
  11P GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           0     5
  11P GAIN WILD-TYPE                        19   129
D18V4, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           5                129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = 12P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    11   0
  12P GAIN WILD-TYPE 145   6
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                11                151 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 0                  6 
$`12P GAIN MUTATED`
TCGA-QR-A6GX TCGA-QR-A6GZ TCGA-QR-A700 TCGA-QR-A70N TCGA-RW-A681 TCGA-S7-A7X1 
       19.04        30.51        32.15         1.41        23.80        18.94 
TCGA-SR-A6MP TCGA-SR-A6MT TCGA-SR-A6MZ TCGA-W2-A7H5 TCGA-WB-A821 
       51.22       106.75        19.76        14.20        93.11 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
       58.88         1.05         9.21        14.17         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D 
       31.53        15.58         1.28         4.11       116.19         0.23 
TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K 
        6.31         2.33        26.83        29.92        13.12         9.01 
TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
      117.14        14.20        41.79         6.02        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       36.23         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        4.41         0.79        13.08        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       50.63         8.09        86.89        19.86         2.93         7.10 
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        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89        20.09        31.59        30.21 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       37.25        35.51        31.04        26.96        40.70        37.58 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 
       30.51        27.91        20.58        25.32        12.66        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
        9.73       114.77       109.25        82.62        67.50       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MS 
       15.52       111.25         1.41         0.10        68.61        81.93 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6N0 TCGA-TT-A6YJ 
      110.53       121.05         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        19.92        13.32        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-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       10.65        34.82        34.26         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      316.73       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 
       41.23        32.61        34.03        33.90        24.16        35.84 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        57.11        38.76        42.54        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       40.04        45.83        53.69        12.99        24.82         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A822 
       23.77        18.28        71.05        78.21        10.16       103.17 
TCGA-XG-A823 
       20.19 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.41               0.10 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            106.75             316.73 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             23.80              20.58 
[1] "1.4 - 106.8 (23.8)" "0.1 - 316.7 (20.6)"
[1] "hr="     "7.4e+07"
D19V2, continuous
D19V3, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    6  5
  12P GAIN WILD-TYPE 82 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      6    5
  12P GAIN WILD-TYPE   82   69
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                6                 82
  MALE                  5                 69
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     0
  12P GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                           2     9
  12P GAIN WILD-TYPE                        17   125
D19V4, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       2                 17
  WHITE                                           9                125
[1] 4 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 = 12Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    14   0
  12Q GAIN WILD-TYPE 142   6
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                14                148 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                  6 
$`12Q GAIN MUTATED`
TCGA-PR-A5PF TCGA-QR-A6GX TCGA-QR-A6GZ TCGA-QR-A700 TCGA-QR-A70N TCGA-RW-A681 
       17.95        19.04        30.51        32.15         1.41        23.80 
TCGA-S7-A7WN TCGA-S7-A7X1 TCGA-SR-A6MP TCGA-SR-A6MT TCGA-SR-A6MZ TCGA-W2-A7H5 
       37.25        18.94        51.22       106.75        19.76        14.20 
TCGA-W2-A7HD TCGA-WB-A821 
       12.49        93.11 

$`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        17.75         5.88        81.70 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU 
       28.08        35.01        23.11         1.25       137.59        58.88 
TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
        1.05         9.21        14.17         9.93        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E 
       15.58         1.28         4.11       116.19         0.23         6.31 
TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70P 
        2.33        26.83        29.92        13.12         9.01       117.14 
TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ 
       14.20        41.79         6.02        12.39        17.95        36.23 
TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP 
        6.94         1.81         0.72        25.18         2.30         4.41 
TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA 
        0.79        13.08        77.98         0.92       108.26        50.63 
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-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
        1.05         0.85        13.32         1.22        11.70        13.05 
TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
        7.96         6.28        72.79        15.02        41.88         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WO 
        1.78         2.89        20.09        31.59        30.21        35.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       31.04        26.96        40.70        37.58        30.51        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       20.58        25.32        12.66        18.08         9.73       114.77 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      109.25        82.62        67.50       110.04        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV 
        1.41         0.10        68.61        81.93       110.53       121.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
        3.12        24.66        49.61         4.34        25.15        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC 
       13.32        25.32        17.16         1.18        19.86        12.03 
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        34.82        34.26 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       316.73       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        41.23        32.61        34.03 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
       33.90        24.16        35.84        37.18        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54        22.32        24.36        40.04        45.83        53.69 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       12.99        24.82         1.61        23.77        18.28        71.05 
TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A822 TCGA-XG-A823 
       78.21        10.16       103.17        20.19 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.41               0.10 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            106.75             316.73 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             21.78              21.45 
[1] "1.4 - 106.8 (21.8)" "0.1 - 316.7 (21.4)"
[1] "hr="     "7.7e+07"
D20V2, continuous
D20V3, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    8  6
  12Q GAIN WILD-TYPE 80 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      8    6
  12Q GAIN WILD-TYPE   80   68
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                8                 80
  MALE                  6                 68
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     0
  12Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                           2    12
  12Q GAIN WILD-TYPE                        17   122
D20V4, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       2                 17
  WHITE                                          12                122
[1] 4 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 = 13Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED     9   0
  13Q GAIN WILD-TYPE 147   6
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 9                153 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 0                  6 
$`13Q GAIN MUTATED`
TCGA-P8-A6RX TCGA-QR-A6GZ TCGA-QR-A70N TCGA-QT-A69Q TCGA-RW-A68F TCGA-S7-A7X1 
       17.75        30.51         1.41         0.79        15.02        18.94 
TCGA-SR-A6MT TCGA-SR-A6N0 TCGA-WB-A821 
      106.75        49.61        93.11 

$`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        17.95        81.70 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU 
       28.08        35.01        23.11         1.25       137.59        58.88 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
       19.04         1.05         9.21        14.17         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       31.53        15.58        32.15         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
        9.01       117.14        14.20        41.79         6.02        12.39 
TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
       17.95        36.23         6.94         1.81         0.72        25.18 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        2.30         4.41        13.08        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       50.63         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-A68G 
       11.70        13.05         7.96         6.28        72.79        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89        20.09        31.59        30.21 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       37.25        35.51        31.04        26.96        40.70        37.58 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 
       30.51        27.91        20.58        25.32        12.66        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
        9.73       114.77       109.25        82.62        67.50       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       15.52       111.25         1.41         0.10        51.22        68.61 
TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
       81.93       110.53       121.05         3.12        24.66        19.76 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        25.15        19.92        13.32        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        34.82        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       316.73       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        41.23        32.61        34.03        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       24.16        35.84        37.18        57.11        38.76        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       22.32        24.36        40.04        45.83        53.69        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        23.77        18.28        71.05        78.21 
TCGA-WB-A820 TCGA-WB-A822 TCGA-XG-A823 
       10.16       103.17        20.19 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.79               0.10 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            106.75             316.73 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             18.94              22.32 
[1] "0.8 - 106.8 (18.9)" "0.1 - 316.7 (22.3)"
[1] "hr="     "2.6e+07"
D21V2, continuous
D21V3, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    4  5
  13Q GAIN WILD-TYPE 84 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    5
  13Q GAIN WILD-TYPE   84   69
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                4                 84
  MALE                  5                 69
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     0
  13Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           1     8
  13Q GAIN WILD-TYPE                        18   126
D21V4, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           8                126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = 14Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED     3   1
  14Q GAIN WILD-TYPE 153   5
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                158 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                  5 
$`14Q GAIN MUTATED`
TCGA-QR-A70N TCGA-RW-A681 TCGA-SR-A6MT TCGA-WB-A820 
        1.41        23.80       106.75        10.16 

$`14Q 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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 
        9.93        14.27        31.53        15.58        32.15         1.28 
TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        4.11       116.19         0.23         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W 
       29.92        13.12         9.01       117.14        14.20        41.79 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
        6.02        12.39        17.95        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        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       77.98         0.92       108.26        50.63         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        41.88         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        30.21        37.25        35.51        31.04 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       26.96        40.70        37.58        30.51        27.91        20.58 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       25.32        12.66        18.94        18.08         9.73       114.77 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      109.25        82.62        67.50       110.04        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU 
        1.41         0.10        51.22        68.61        81.93       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      121.05         3.12        24.66        19.76        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       25.15        19.92        13.32        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        34.82        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       316.73       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        41.23        32.61        34.03        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       24.36        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 
        1.61        23.77        18.28        71.05        78.21        93.11 
TCGA-WB-A822 TCGA-XG-A823 
      103.17        20.19 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1.41               0.10 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            106.75             316.73 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             16.98              21.45 
[1] "1.4 - 106.8 (17.0)" "0.1 - 316.7 (21.4)"
[1] "hr=" "12" 
D22V2, continuous
D22V3, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    1  3
  14Q GAIN WILD-TYPE 87 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1    3
  14Q GAIN WILD-TYPE   87   71
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                1                 87
  MALE                  3                 71
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     0
  14Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           1     3
  14Q GAIN WILD-TYPE                        18   131
D22V4, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           3                131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = 15Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    14   0
  15Q GAIN WILD-TYPE 142   6
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                148 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 0                  6 
$`15Q GAIN MUTATED`
TCGA-QR-A6GX TCGA-QR-A700 TCGA-QR-A70N TCGA-QR-A7IN TCGA-RW-A681 TCGA-S7-A7WN 
       19.04        32.15         1.41        12.39        23.80        37.25 
TCGA-S7-A7WW TCGA-S7-A7X1 TCGA-SP-A6QF TCGA-W2-A7H5 TCGA-W2-A7UY TCGA-WB-A80L 
       20.58        18.94        82.62        14.20        10.65        34.26 
TCGA-WB-A81A TCGA-WB-A81D 
       24.16        35.84 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       58.88         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       14.27        31.53        15.58         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IP 
        9.01       117.14        14.20        41.79         6.02        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       36.23         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        4.41         0.79        13.08        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       50.63         8.09        86.89        19.86         2.93         7.10 
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        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89        20.09        31.59        30.21 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       35.51        31.04        26.96        40.70        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       27.91        25.32        12.66        18.08         9.73       114.77 
TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
      109.25        67.50       110.04        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
        0.10        51.22        68.61        81.93       106.75       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      121.05         3.12        24.66        19.76        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA 
       25.15        19.92        13.32        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-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       34.82         4.47         4.73         4.21       316.73       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        41.23        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       34.03        33.90        37.18        57.11        38.76        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       22.32        24.36        40.04        45.83        53.69        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        23.77        18.28        71.05        78.21 
TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       10.16        93.11       103.17        20.19 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1.41               0.10 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             82.62             316.73 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            22.190             21.255 
[1] "1.4 - 82.6 (22.2)"  "0.1 - 316.7 (21.3)"
[1] "hr="     "7.7e+07"
D23V2, continuous
D23V3, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    7  7
  15Q GAIN WILD-TYPE 81 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      7    7
  15Q GAIN WILD-TYPE   81   67
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                7                 81
  MALE                  7                 67
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     1
  15Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           3    10
  15Q GAIN WILD-TYPE                        16   124
D23V4, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       3                 16
  WHITE                                          10                124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = 16P GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED     6   0
  16P GAIN WILD-TYPE 150   6
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                156 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 0                  6 
$`16P GAIN MUTATED`
TCGA-QR-A6GX TCGA-RW-A681 TCGA-RX-A8JQ TCGA-SR-A6MP TCGA-W2-A7H5 TCGA-WB-A81A 
       19.04        23.80        20.09        51.22        14.20        24.16 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       58.88         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 
       14.27        31.53        15.58        32.15         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
      116.19         0.23         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W 
       13.12         9.01         1.41       117.14        14.20        41.79 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
        6.02        12.39        17.95        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        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       77.98         0.92       108.26        50.63         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        41.88         4.41         1.78         2.89 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       31.59        30.21        37.25        35.51        31.04        26.96 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       40.70        37.58        30.51        27.91        20.58        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       12.66        18.94        18.08         9.73       114.77       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       82.62        67.50       110.04        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
        0.10        68.61        81.93       106.75       110.53       121.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        19.76        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
       19.92        13.32        25.32        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 
       34.82        34.26         4.47         4.73         4.21       316.73 
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        41.23 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       32.61        34.03        33.90        35.84        37.18        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        42.54        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       53.69        12.99        24.82         1.61        23.77        18.28 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        78.21        10.16        93.11       103.17        20.19 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              14.2                0.1 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             51.22             316.73 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            21.945             21.450 
[1] "14.2 - 51.2 (21.9)" "0.1 - 316.7 (21.4)"
[1] "hr="     "2.6e+07"
D24V2, continuous
D24V3, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    4  2
  16P GAIN WILD-TYPE 84 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4    2
  16P GAIN WILD-TYPE   84   72
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                4                 84
  MALE                  2                 72
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  0     0
  16P GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                           1     5
  16P GAIN WILD-TYPE                        18   129
D24V4, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           5                129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = 16Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED     5   1
  16Q GAIN WILD-TYPE 151   5
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                156 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                  5 
$`16Q GAIN MUTATED`
TCGA-QR-A6GX TCGA-RW-A681 TCGA-RX-A8JQ TCGA-SR-A6MP TCGA-W2-A7H5 TCGA-WB-A820 
       19.04        23.80        20.09        51.22        14.20        10.16 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       58.88         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 
       14.27        31.53        15.58        32.15         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
      116.19         0.23         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W 
       13.12         9.01         1.41       117.14        14.20        41.79 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
        6.02        12.39        17.95        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        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       77.98         0.92       108.26        50.63         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        41.88         4.41         1.78         2.89 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       31.59        30.21        37.25        35.51        31.04        26.96 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       40.70        37.58        30.51        27.91        20.58        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       12.66        18.94        18.08         9.73       114.77       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       82.62        67.50       110.04        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
        0.10        68.61        81.93       106.75       110.53       121.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        19.76        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
       19.92        13.32        25.32        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 
       34.82        34.26         4.47         4.73         4.21       316.73 
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        41.23 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        34.03        33.90        24.16        35.84        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       57.11        38.76        42.54        22.32        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       45.83        53.69        12.99        24.82         1.61        23.77 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       18.28        71.05        78.21        93.11       103.17        20.19 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             10.16               0.10 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             51.22             316.73 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            19.565             22.715 
[1] "10.2 - 51.2 (19.6)" "0.1 - 316.7 (22.7)"
[1] "hr=" "6.7"
D25V2, continuous
D25V3, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3  3
  16Q GAIN WILD-TYPE 85 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    3
  16Q GAIN WILD-TYPE   85   71
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                3                 85
  MALE                  3                 71
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  0     0
  16Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                           1     5
  16Q GAIN WILD-TYPE                        18   129
D25V4, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           5                129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = 17Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED     5   0
  17Q GAIN WILD-TYPE 151   6
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                157 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 0                  6 
$`17Q GAIN MUTATED`
TCGA-QR-A70K TCGA-QT-A5XP TCGA-RW-A681 TCGA-WB-A81J TCGA-WB-A81W 
        9.01         4.41        23.80        24.36        78.21 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 
        9.93        14.27        31.53        15.58        32.15         1.28 
TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        4.11       116.19         0.23         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W 
       29.92        13.12         1.41       117.14        14.20        41.79 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
        6.02        12.39        17.95        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        13.08        77.98 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92       108.26        50.63         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        41.88         4.41         1.78         2.89        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       31.59        30.21        37.25        35.51        31.04        26.96 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       40.70        37.58        30.51        27.91        20.58        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       12.66        18.94        18.08         9.73       114.77       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       82.62        67.50       110.04        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
        0.10        51.22        68.61        81.93       106.75       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      121.05         3.12        24.66        19.76        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       25.15        19.92        13.32        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        34.82        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       316.73       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        41.23        32.61        34.03        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       40.04        45.83        53.69        12.99        24.82         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 
       23.77        18.28        71.05        10.16        93.11       103.17 
TCGA-XG-A823 
       20.19 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              4.41               0.10 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             78.21             316.73 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             23.80              20.58 
[1] "4.4 - 78.2 (23.8)"  "0.1 - 316.7 (20.6)"
[1] "hr="     "2.5e+07"
D26V2, continuous
D26V3, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    1  4
  17Q GAIN WILD-TYPE 87 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1    4
  17Q GAIN WILD-TYPE   87   70
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                1                 87
  MALE                  4                 70
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0     0
  17Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                           1     4
  17Q GAIN WILD-TYPE                        18   130
D26V4, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           4                130
[1] 4 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 = 18P GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED     8   0
  18P GAIN WILD-TYPE 148   6
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 8                154 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                  6 
$`18P GAIN MUTATED`
TCGA-QR-A6GZ TCGA-QR-A700 TCGA-QR-A70N TCGA-QR-A70W TCGA-RT-A6YA TCGA-RW-A681 
       30.51        32.15         1.41        41.79        50.63        23.80 
TCGA-SR-A6MT TCGA-WB-A80L 
      106.75        34.26 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       58.88        19.04         1.05         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       14.27        31.53        15.58         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
        9.01       117.14        14.20         6.02        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       36.23         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        4.41         0.79        13.08        77.98         0.92       108.26 
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-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
        1.05         0.85        13.32         1.22        11.70        13.05 
TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
        7.96         6.28        72.79        15.02        41.88         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89        20.09        31.59        30.21        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       35.51        31.04        26.96        40.70        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       27.91        20.58        25.32        12.66        18.94        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
        9.73       114.77       109.25        82.62        67.50       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       15.52       111.25         1.41         0.10        51.22        68.61 
TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
       81.93       110.53       121.05         3.12        24.66        19.76 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15        19.92        13.32        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        34.82         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       316.73       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        41.23        32.61        34.03        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       24.16        35.84        37.18        57.11        38.76        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       22.32        24.36        40.04        45.83        53.69        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        23.77        18.28        71.05        78.21 
TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       10.16        93.11       103.17        20.19 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              1.41               0.10 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            106.75             316.73 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            33.205             20.005 
[1] "1.4 - 106.8 (33.2)" "0.1 - 316.7 (20.0)"
[1] "hr="     "2.7e+07"
D27V2, continuous
D27V3, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    3  5
  18P GAIN WILD-TYPE 85 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3    5
  18P GAIN WILD-TYPE   85   69
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                3                 85
  MALE                  5                 69
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     0
  18P GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           1     7
  18P GAIN WILD-TYPE                        18   127
D27V4, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           7                127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = 18Q GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    10   0
  18Q GAIN WILD-TYPE 146   6
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                152 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                  6 
$`18Q GAIN MUTATED`
TCGA-P8-A5KD TCGA-QR-A6GZ TCGA-QR-A700 TCGA-QR-A70N TCGA-RT-A6YA TCGA-RW-A681 
        2.27        30.51        32.15         1.41        50.63        23.80 
TCGA-SR-A6MS TCGA-SR-A6MT TCGA-WB-A80L TCGA-WB-A81W 
       81.93       106.75        34.26        78.21 

$`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        17.75         5.88        17.95        81.70 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU 
       28.08        35.01        23.11         1.25       137.59        58.88 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
       19.04         1.05         9.21        14.17         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D 
       31.53        15.58         1.28         4.11       116.19         0.23 
TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K 
        6.31         2.33        26.83        29.92        13.12         9.01 
TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
      117.14        14.20        41.79         6.02        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       36.23         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        4.41         0.79        13.08        77.98         0.92       108.26 
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-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
        1.05         0.85        13.32         1.22        11.70        13.05 
TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
        7.96         6.28        72.79        15.02        41.88         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89        20.09        31.59        30.21        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       35.51        31.04        26.96        40.70        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       27.91        20.58        25.32        12.66        18.94        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
        9.73       114.77       109.25        82.62        67.50       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       15.52       111.25         1.41         0.10        51.22        68.61 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
      110.53       121.05         3.12        24.66        19.76        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        25.15        19.92        13.32        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-A80N 
       17.69        25.61        10.65        34.82         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       316.73       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        41.23        32.61        34.03        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       24.36        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A820 TCGA-WB-A821 
        1.61        23.77        18.28        71.05        10.16        93.11 
TCGA-WB-A822 TCGA-XG-A823 
      103.17        20.19 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              1.41               0.10 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            106.75             316.73 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            33.205             20.005 
[1] "1.4 - 106.8 (33.2)" "0.1 - 316.7 (20.0)"
[1] "hr="     "7.5e+07"
D28V2, continuous
D28V3, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    5  5
  18Q GAIN WILD-TYPE 83 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    5
  18Q GAIN WILD-TYPE   83   69
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                5                 83
  MALE                  5                 69
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     0
  18Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           1     9
  18Q GAIN WILD-TYPE                        18   125
D28V4, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           9                125
[1] 4 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 = 19P GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    19   1
  19P GAIN WILD-TYPE 137   5
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                20                142 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 1                  5 
$`19P GAIN MUTATED`
TCGA-QR-A6GX TCGA-QR-A6GZ TCGA-QR-A6H6 TCGA-QR-A70N TCGA-RT-A6YA TCGA-RW-A681 
       19.04        30.51        15.58         1.41        50.63        23.80 
TCGA-S7-A7WP TCGA-S7-A7WW TCGA-SQ-A6I6 TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6N0 
       31.04        20.58         0.10        81.93       106.75        49.61 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-WB-A80L TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81H 
       25.32        14.20        34.26        34.03        24.16        42.54 
TCGA-WB-A81Q TCGA-WB-A81S 
       24.82        23.77 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
       58.88         1.05         9.21        14.17         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D 
       31.53        32.15         1.28         4.11       116.19         0.23 
TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K 
        6.31         2.33        26.83        29.92        13.12         9.01 
TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
      117.14        14.20        41.79         6.02        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       36.23         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        4.41         0.79        13.08        77.98         0.92       108.26 
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-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
        1.05         0.85        13.32         1.22        11.70        13.05 
TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
        7.96         6.28        72.79        15.02        41.88         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89        20.09        31.59        30.21        37.25 
TCGA-S7-A7WO TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       35.51        26.96        40.70        37.58        30.51        27.91 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       25.32        12.66        18.94        18.08         9.73       114.77 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      109.25        82.62        67.50       110.04        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX 
        1.41        51.22        68.61       110.53       121.05         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       24.66        19.76         4.34        25.15        19.92        13.32 
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-A80M TCGA-WB-A80N 
       17.69        25.61        10.65        34.82         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       316.73       127.56        29.16        19.59        32.88 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81E 
        5.98        41.23        32.61        33.90        35.84        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       57.11        38.76        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       53.69        12.99         1.61        18.28        71.05        78.21 
TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       10.16        93.11       103.17        20.19 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.10               0.23 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            106.75             316.73 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             25.07              19.86 
[1] "0.1 - 106.8 (25.1)" "0.2 - 316.7 (19.9)"
[1] "hr=" "1.5"
D29V2, continuous
D29V3, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   12  8
  19P GAIN WILD-TYPE 76 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     12    8
  19P GAIN WILD-TYPE   76   66
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               12                 76
  MALE                  8                 66
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     0
  19P GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           2    18
  19P GAIN WILD-TYPE                        17   116
D29V4, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       2                 17
  WHITE                                          18                116
[1] 4 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 = 19Q GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    14   0
  19Q GAIN WILD-TYPE 142   6
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                14                148 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                  6 
$`19Q GAIN MUTATED`
TCGA-QR-A6GX TCGA-QR-A6GZ TCGA-QR-A70N TCGA-RW-A681 TCGA-S7-A7WW TCGA-SQ-A6I6 
       19.04        30.51         1.41        23.80        20.58         0.10 
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        34.26        34.03 
TCGA-WB-A81A TCGA-WB-A81H 
       24.16        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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
       58.88         1.05         9.21        14.17         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       31.53        15.58        32.15         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
        9.01       117.14        14.20        41.79         6.02        12.39 
TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
       17.95        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        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
      108.26        50.63         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 
       41.88         4.41         1.78         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       30.21        37.25        35.51        31.04        26.96        40.70 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 
       37.58        30.51        27.91        25.32        12.66        18.94 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       18.08         9.73       114.77       109.25        82.62        67.50 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MQ 
      110.04        15.52       111.25         1.41        51.22        68.61 
TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
       81.93       110.53       121.05         3.12        24.66        19.76 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7H7 TCGA-W2-A7HA 
        4.34        25.15        19.92        13.32        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        34.82         4.47         4.73         4.21       316.73 
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        41.23 
TCGA-WB-A817 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
       32.61        33.90        35.84        37.18        57.11        38.76 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       22.32        24.36        40.04        45.83        53.69        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        23.77        18.28        71.05        78.21 
TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       10.16        93.11       103.17        20.19 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.10               0.23 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            106.75             316.73 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            24.740             20.005 
[1] "0.1 - 106.8 (24.7)" "0.2 - 316.7 (20.0)"
[1] "hr="     "7.7e+07"
D30V2, continuous
D30V3, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    8  6
  19Q GAIN WILD-TYPE 80 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      8    6
  19Q GAIN WILD-TYPE   80   68
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                8                 80
  MALE                  6                 68
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     0
  19Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           2    12
  19Q GAIN WILD-TYPE                        17   122
D30V4, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       2                 17
  WHITE                                          12                122
[1] 4 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 = 20P GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    12   0
  20P GAIN WILD-TYPE 144   6
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                150 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 0                  6 
$`20P GAIN MUTATED`
TCGA-PR-A5PF TCGA-QR-A6GZ TCGA-QR-A700 TCGA-RM-A68W TCGA-RW-A681 TCGA-SP-A6QI 
       17.95        30.51        32.15         0.92        23.80       110.04 
TCGA-SR-A6MT TCGA-TT-A6YN TCGA-WB-A80L TCGA-WB-A80N TCGA-WB-A81A TCGA-WB-A821 
      106.75        19.92        34.26         4.73        24.16        93.11 

$`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        17.75         5.88        81.70 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU 
       28.08        35.01        23.11         1.25       137.59        58.88 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
       19.04         1.05         9.21        14.17         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D 
       31.53        15.58         1.28         4.11       116.19         0.23 
TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K 
        6.31         2.33        26.83        29.92        13.12         9.01 
TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
        1.41       117.14        14.20        41.79         6.02        12.39 
TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
       17.95        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        13.08        77.98       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       50.63         8.09        86.89        19.86         2.93         7.10 
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        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89        20.09        31.59        30.21 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       37.25        35.51        31.04        26.96        40.70        37.58 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 
       30.51        27.91        20.58        25.32        12.66        18.94 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       18.08         9.73       114.77       109.25        82.62        67.50 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       15.52       111.25         1.41         0.10        51.22        68.61 
TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
       81.93       110.53       121.05         3.12        24.66        19.76 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
       49.61         4.34        25.15        13.32        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        34.82         4.47         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      316.73       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 
       41.23        32.61        34.03        33.90        35.84        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       57.11        38.76        42.54        22.32        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       45.83        53.69        12.99        24.82         1.61        23.77 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A822 TCGA-XG-A823 
       18.28        71.05        78.21        10.16       103.17        20.19 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.92               0.10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            110.04             316.73 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            27.335             20.140 
[1] "0.9 - 110.0 (27.3)" "0.1 - 316.7 (20.1)"
[1] "hr="     "7.6e+07"
D31V2, continuous
D31V3, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    7  5
  20P GAIN WILD-TYPE 81 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7    5
  20P GAIN WILD-TYPE   81   69
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                7                 81
  MALE                  5                 69
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0     0
  20P GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                           0    12
  20P GAIN WILD-TYPE                        19   122
D31V4, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                          12                122
[1] 4 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 = 20Q GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    10   0
  20Q GAIN WILD-TYPE 146   6
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                152 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 0                  6 
$`20Q GAIN MUTATED`
TCGA-PR-A5PF TCGA-QR-A6GX TCGA-QR-A6GZ TCGA-QR-A700 TCGA-RW-A681 TCGA-SP-A6QI 
       17.95        19.04        30.51        32.15        23.80       110.04 
TCGA-SR-A6MT TCGA-WB-A80L TCGA-WB-A81A TCGA-WB-A821 
      106.75        34.26        24.16        93.11 

$`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        17.75         5.88        81.70 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU 
       28.08        35.01        23.11         1.25       137.59        58.88 
TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
        1.05         9.21        14.17         9.93        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E 
       15.58         1.28         4.11       116.19         0.23         6.31 
TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N 
        2.33        26.83        29.92        13.12         9.01         1.41 
TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
      117.14        14.20        41.79         6.02        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       36.23         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        4.41         0.79        13.08        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       50.63         8.09        86.89        19.86         2.93         7.10 
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        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89        20.09        31.59        30.21 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       37.25        35.51        31.04        26.96        40.70        37.58 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 
       30.51        27.91        20.58        25.32        12.66        18.94 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       18.08         9.73       114.77       109.25        82.62        67.50 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       15.52       111.25         1.41         0.10        51.22        68.61 
TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
       81.93       110.53       121.05         3.12        24.66        19.76 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15        19.92        13.32        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        34.82         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       316.73       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        41.23        32.61        34.03        33.90 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       24.36        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
        1.61        23.77        18.28        71.05        78.21        10.16 
TCGA-WB-A822 TCGA-XG-A823 
      103.17        20.19 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             17.95               0.10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            110.04             316.73 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            31.330             20.005 
[1] "17.9 - 110.0 (31.3)" "0.1 - 316.7 (20.0)" 
[1] "hr="     "7.5e+07"
D32V2, continuous
D32V3, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    6  4
  20Q GAIN WILD-TYPE 82 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      6    4
  20Q GAIN WILD-TYPE   82   70
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                6                 82
  MALE                  4                 70
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0     0
  20Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                           1     9
  20Q GAIN WILD-TYPE                        18   125
D32V4, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           9                125
[1] 4 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 = 21Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED     3   0
  21Q GAIN WILD-TYPE 153   6
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                159 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 0                  6 
$`21Q GAIN MUTATED`
TCGA-QR-A6GX TCGA-QR-A6GZ TCGA-S7-A7X1 
       19.04        30.51        18.94 

$`21Q 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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
       58.88         1.05         9.21        14.17         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       31.53        15.58        32.15         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
        9.01         1.41       117.14        14.20        41.79         6.02 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       12.39        17.95        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        13.08        77.98 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92       108.26        50.63         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        41.88         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        30.21        37.25        35.51        31.04 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       26.96        40.70        37.58        30.51        27.91        20.58 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       25.32        12.66        18.08         9.73       114.77       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       82.62        67.50       110.04        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
        0.10        51.22        68.61        81.93       106.75       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      121.05         3.12        24.66        19.76        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       25.15        19.92        13.32        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        34.82        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       316.73       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        41.23        32.61        34.03        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       24.36        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
        1.61        23.77        18.28        71.05        78.21        10.16 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       93.11       103.17        20.19 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             18.94               0.10 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             30.51             316.73 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             19.04              22.32 
[1] "18.9 - 30.5 (19.0)" "0.1 - 316.7 (22.3)"
[1] "hr="     "9200000"
D33V2, continuous
D33V3, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    1  2
  21Q GAIN WILD-TYPE 87 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1    2
  21Q GAIN WILD-TYPE   87   72
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                1                 87
  MALE                  2                 72
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  0     0
  21Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           1     2
  21Q GAIN WILD-TYPE                        18   132
D33V4, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           2                132
[1] 4 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 = 22Q GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED     3   0
  22Q GAIN WILD-TYPE 153   6
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                159 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 0                  6 
$`22Q GAIN MUTATED`
TCGA-QR-A700 TCGA-QR-A70N TCGA-SR-A6MT 
       32.15         1.41       106.75 

$`22Q 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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 
        9.93        14.27        31.53        15.58         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
      116.19         0.23         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
       13.12         9.01       117.14        14.20        41.79         6.02 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       12.39        17.95        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        13.08        77.98 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92       108.26        50.63         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        41.88         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        30.21        37.25        35.51        31.04 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       26.96        40.70        37.58        30.51        27.91        20.58 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       25.32        12.66        18.94        18.08         9.73       114.77 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      109.25        82.62        67.50       110.04        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU 
        1.41         0.10        51.22        68.61        81.93       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      121.05         3.12        24.66        19.76        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       25.15        19.92        13.32        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        34.82        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       316.73       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        41.23        32.61        34.03        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       24.36        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
        1.61        23.77        18.28        71.05        78.21        10.16 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       93.11       103.17        20.19 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1.41               0.10 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            106.75             316.73 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             32.15              20.58 
[1] "1.4 - 106.8 (32.1)" "0.1 - 316.7 (20.6)"
[1] "hr="     "9200000"
D34V2, continuous
D34V3, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    1  2
  22Q GAIN WILD-TYPE 87 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1    2
  22Q GAIN WILD-TYPE   87   72
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                1                 87
  MALE                  2                 72
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0     0
  22Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           1     2
  22Q GAIN WILD-TYPE                        18   132
D34V4, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           2                132
[1] 4 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 = XP GAIN MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED     6   0
  XP GAIN WILD-TYPE 150   6
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                6               156 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                0                 6 
$`XP GAIN MUTATED`
TCGA-QR-A6GX TCGA-QR-A70C TCGA-RW-A681 TCGA-SR-A6MT TCGA-WB-A80L TCGA-WB-A81A 
       19.04       116.19        23.80       106.75        34.26        24.16 

$`XP 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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       58.88         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 
       14.27        31.53        15.58        32.15         1.28         4.11 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
        9.01         1.41       117.14        14.20        41.79         6.02 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       12.39        17.95        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        13.08        77.98 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92       108.26        50.63         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        41.88         4.41         1.78         2.89        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       31.59        30.21        37.25        35.51        31.04        26.96 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       40.70        37.58        30.51        27.91        20.58        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       12.66        18.94        18.08         9.73       114.77       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       82.62        67.50       110.04        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV 
        0.10        51.22        68.61        81.93       110.53       121.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        19.76        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       19.92        13.32        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        34.82         4.47         4.73         4.21       316.73 
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        41.23 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       32.61        34.03        33.90        35.84        37.18        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        42.54        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       53.69        12.99        24.82         1.61        23.77        18.28 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        78.21        10.16        93.11       103.17        20.19 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
            19.04              0.10 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           116.19            316.73 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            29.21             20.14 
[1] "19.0 - 116.2 (29.2)" "0.1 - 316.7 (20.1)" 
[1] "hr="     "2.6e+07"
D35V2, continuous
D35V3, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    5  1
  XP GAIN WILD-TYPE 83 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      5    1
  XP GAIN WILD-TYPE   83   73
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE               5                83
  MALE                 1                73
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP GAIN MUTATED                                  0     0
  XP GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED                           2     4
  XP GAIN WILD-TYPE                        17   130
D35V4, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          4               130
[1] 4 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 = XQ GAIN MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED     5   0
  XQ GAIN WILD-TYPE 151   6
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                5               157 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                0                 6 
$`XQ GAIN MUTATED`
TCGA-QR-A6GX TCGA-RW-A681 TCGA-SR-A6MT TCGA-WB-A80L TCGA-WB-A81A 
       19.04        23.80       106.75        34.26        24.16 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       58.88         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 
       14.27        31.53        15.58        32.15         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
      116.19         0.23         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W 
       13.12         9.01         1.41       117.14        14.20        41.79 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
        6.02        12.39        17.95        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        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       77.98         0.92       108.26        50.63         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        41.88         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        30.21        37.25        35.51        31.04 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       26.96        40.70        37.58        30.51        27.91        20.58 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       25.32        12.66        18.94        18.08         9.73       114.77 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      109.25        82.62        67.50       110.04        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU 
        1.41         0.10        51.22        68.61        81.93       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      121.05         3.12        24.66        19.76        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       25.15        19.92        13.32        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-A80M TCGA-WB-A80N TCGA-WB-A80O 
       25.61        10.65        34.82         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      316.73       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 
       41.23        32.61        34.03        33.90        35.84        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       57.11        38.76        42.54        22.32        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       45.83        53.69        12.99        24.82         1.61        23.77 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 
       18.28        71.05        78.21        10.16        93.11       103.17 
TCGA-XG-A823 
       20.19 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            19.04              0.10 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           106.75            316.73 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            24.16             20.19 
[1] "19.0 - 106.8 (24.2)" "0.1 - 316.7 (20.2)" 
[1] "hr="     "2.6e+07"
D36V2, continuous
D36V3, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    4  1
  XQ GAIN WILD-TYPE 84 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      4    1
  XQ GAIN WILD-TYPE   84   73
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               4                84
  MALE                 1                73
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     0
  XQ GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                           1     4
  XQ GAIN WILD-TYPE                        18   130
D36V4, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          4               130
[1] 4 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 = 1P LOSS MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   96  2
  1P LOSS WILD-TYPE 60  4
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               98                64 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                 4 
$`1P LOSS MUTATED`
TCGA-P7-A5NY TCGA-P8-A5KD TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO 
       31.46         2.27        17.95        81.70        28.08        35.01 
TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
      137.59        19.04         9.21        14.17         9.93        14.27 
TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70H TCGA-QR-A70J 
       15.58        32.15         0.23         6.31        26.83        13.12 
TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
        9.01       117.14        14.20        41.79         6.02        12.39 
TCGA-QR-A7IP TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RM-A68T 
       17.95         6.94         0.72         2.30         0.79        77.98 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A680 
       50.63         8.09        86.89        19.86         7.10        33.30 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
        1.05         0.85        13.32         1.22        11.70        13.05 
TCGA-RW-A68B TCGA-RW-A7D0 TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WQ TCGA-S7-A7WR 
        7.96         1.78        20.09        37.25        26.96        40.70 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QF TCGA-SP-A6QG 
       25.32        12.66        18.94        18.08        82.62        67.50 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MQ 
      110.04        15.52       111.25         1.41         0.10        68.61 
TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ 
       81.93       106.75       110.53        24.66        19.76         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
       25.15        19.92        14.20        17.16         1.18        19.86 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7UY TCGA-WB-A80M 
       12.03        12.49        16.60        17.69        10.65         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A816 TCGA-WB-A818 
        4.73         4.21       316.73        29.16        41.23        34.03 
TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81K 
       33.90        35.84        37.18        38.76        42.54        40.04 
TCGA-WB-A81M TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       45.83        24.82         1.61        18.28        71.05        78.21 
TCGA-WB-A821 TCGA-WB-A822 
       93.11       103.17 

$`1P LOSS WILD-TYPE`
TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GU 
       29.03        17.75         5.88        23.11         1.25        58.88 
TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H5 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
        1.05        30.51        31.53         1.28         4.11       116.19 
TCGA-QR-A70G TCGA-QR-A70I TCGA-QR-A70N TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A5XN 
        2.33        29.92         1.41        36.23         1.81        25.18 
TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RW-A67X TCGA-RW-A681 
        4.41        13.08         0.92       108.26         2.93        23.80 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A8AZ 
        6.28        72.79        15.02        41.88         4.41         2.89 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WT TCGA-S7-A7WU 
       31.59        30.21        35.51        31.04        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SR-A6MP 
       27.91        20.58         9.73       114.77       109.25        51.22 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HH 
      121.05         3.12        49.61        13.32        25.32        25.61 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
       34.82        34.26       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        24.16        57.11        22.32        24.36        53.69 
TCGA-WB-A81P TCGA-WB-A81S TCGA-WB-A820 TCGA-XG-A823 
       12.99        23.77        10.16        20.19 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.10              0.92 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           316.73            127.56 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            18.99             24.77 
[1] "0.1 - 316.7 (19.0)" "0.9 - 127.6 (24.8)"
[1] "hr=" "2.8"
D37V2, continuous
D37V3, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   52 46
  1P LOSS WILD-TYPE 36 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     52   46
  1P LOSS WILD-TYPE   36   28
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              52                36
  MALE                46                28
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  1     4
  1P LOSS WILD-TYPE                                0     1
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           8    83
  1P LOSS WILD-TYPE                        11    51
D37V4, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          4                 1
  BLACK OR AFRICAN AMERICAN                      8                11
  WHITE                                         83                51
[1] 4 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 = 1Q LOSS MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    26   1
  1Q LOSS WILD-TYPE 130   5
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               27               135 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1                 5 
$`1Q LOSS MUTATED`
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70E 
        9.93        14.27        15.58        32.15         0.23         6.31 
TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70X TCGA-QR-A7IN TCGA-QT-A5XM TCGA-QT-A5XO 
        9.01       117.14         6.02        12.39         0.72         2.30 
TCGA-QT-A69Q TCGA-RM-A68T TCGA-RW-A688 TCGA-RW-A68A TCGA-RX-A8JQ TCGA-S7-A7WQ 
        0.79        77.98         1.22        13.05        20.09        26.96 
TCGA-S7-A7X1 TCGA-SP-A6QF TCGA-SR-A6MT TCGA-SR-A6MY TCGA-W2-A7H7 TCGA-WB-A81D 
       18.94        82.62       106.75        24.66        17.16        35.84 
TCGA-WB-A81E TCGA-WB-A81K TCGA-WB-A821 
       37.18        40.04        93.11 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H5 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70G TCGA-QR-A70H 
       31.53         1.28         4.11       116.19         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A7IP 
       29.92        13.12         1.41        14.20        41.79        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A7U0 
       36.23         6.94         1.81        25.18         4.41        13.08 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92       108.26        50.63         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-A689 TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F 
       13.32        11.70         7.96         6.28        72.79        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-S7-A7WL TCGA-S7-A7WM 
       41.88         4.41         1.78         2.89        31.59        30.21 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       37.25        35.51        31.04        40.70        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 
       27.91        20.58        25.32        12.66        18.08         9.73 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      114.77       109.25        67.50       110.04        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU 
        1.41         0.10        51.22        68.61        81.93       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
      121.05         3.12        19.76        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HB 
       19.92        13.32        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-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       34.82        34.26         4.47         4.73         4.21       316.73 
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        41.23 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81F TCGA-WB-A81G 
       32.61        34.03        33.90        24.16        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       42.54        22.32        24.36        45.83        53.69        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        23.77        18.28        71.05        78.21 
TCGA-WB-A820 TCGA-WB-A822 TCGA-XG-A823 
       10.16       103.17        20.19 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.23              0.10 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           117.14            316.73 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            17.16             23.77 
[1] "0.2 - 117.1 (17.2)" "0.1 - 316.7 (23.8)"
[1] "hr=" "1.1"
D38V2, continuous
D38V3, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED   13 14
  1Q LOSS WILD-TYPE 75 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     13   14
  1Q LOSS WILD-TYPE   75   60
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              13                75
  MALE                14                60
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     2
  1Q LOSS WILD-TYPE                                1     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           5    20
  1Q LOSS WILD-TYPE                        14   114
D38V4, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 3
  BLACK OR AFRICAN AMERICAN                      5                14
  WHITE                                         20               114
[1] 4 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 = 2P LOSS MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    10   0
  2P LOSS WILD-TYPE 146   6
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               152 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                0                 6 
$`2P LOSS MUTATED`
TCGA-QR-A6GY TCGA-QR-A6H2 TCGA-QR-A70R TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RW-A68G 
        1.05         9.93        14.20         2.30         0.79        41.88 
TCGA-S7-A7X0 TCGA-W2-A7HB TCGA-WB-A815 TCGA-WB-A821 
       12.66        19.86         5.98        93.11 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H3 
       58.88        19.04        30.51         9.21        14.17        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       31.53        15.58        32.15         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
        9.01         1.41       117.14        41.79         6.02        12.39 
TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
       17.95        36.23         6.94         1.81         0.72        25.18 
TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA 
        4.41        13.08        77.98         0.92       108.26        50.63 
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-A688 TCGA-RW-A689 
       23.80         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-A7CZ 
       13.05         7.96         6.28        72.79        15.02         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89        20.09        31.59        30.21        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       35.51        31.04        26.96        40.70        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 
       27.91        20.58        25.32        18.94        18.08         9.73 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      114.77       109.25        82.62        67.50       110.04        15.52 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
      111.25         1.41         0.10        51.22        68.61        81.93 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
      106.75       110.53       121.05         3.12        24.66        19.76 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15        19.92        13.32        25.32 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       14.20        17.16         1.18        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        34.82        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       316.73       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        41.23        32.61        34.03        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       24.36        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
        1.61        23.77        18.28        71.05        78.21        10.16 
TCGA-WB-A822 TCGA-XG-A823 
      103.17        20.19 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.79              0.10 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            93.11            316.73 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           11.295            23.785 
[1] "0.8 - 93.1 (11.3)"  "0.1 - 316.7 (23.8)"
[1] "hr="     "2.6e+07"
D39V2, continuous
D39V3, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    5  5
  2P LOSS WILD-TYPE 83 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5    5
  2P LOSS WILD-TYPE   83   69
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               5                83
  MALE                 5                69
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     1
  2P LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           1     8
  2P LOSS WILD-TYPE                        18   126
D39V4, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          8               126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = 2Q LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    12   1
  2Q LOSS WILD-TYPE 144   5
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               13               149 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                 5 
$`2Q LOSS MUTATED`
TCGA-QR-A6GT TCGA-QR-A6H2 TCGA-QR-A6H6 TCGA-QR-A70K TCGA-QR-A7IP TCGA-QT-A5XO 
      137.59         9.93        15.58         9.01        17.95         2.30 
TCGA-QT-A69Q TCGA-S7-A7X0 TCGA-SP-A6QC TCGA-SP-A6QG TCGA-SR-A6MX TCGA-W2-A7HB 
        0.79        12.66       114.77        67.50         3.12        19.86 
TCGA-WB-A821 
       93.11 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GU 
       81.70        28.08        35.01        23.11         1.25        58.88 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H3 
       19.04         1.05        30.51         9.21        14.17        14.27 
TCGA-QR-A6H5 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D 
       31.53        32.15         1.28         4.11       116.19         0.23 
TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N 
        6.31         2.33        26.83        29.92        13.12         1.41 
TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QT-A5XJ 
      117.14        14.20        41.79         6.02        12.39        36.23 
TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A7U0 
        6.94         1.81         0.72        25.18         4.41        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       77.98         0.92       108.26        50.63         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        41.88         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89        20.09        31.59        30.21        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       31.04        26.96        40.70        37.58        30.51        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QD 
       20.58        25.32        18.94        18.08         9.73       109.25 
TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       82.62       110.04        15.52       111.25         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
       51.22        68.61        81.93       106.75       110.53       121.05 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        19.76        49.61         4.34        25.15        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC 
       13.32        25.32        14.20        17.16         1.18        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        34.82 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       34.26         4.47         4.73         4.21       316.73       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        41.23        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       34.03        33.90        24.16        35.84        37.18        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        42.54        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       53.69        12.99        24.82         1.61        23.77        18.28 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A822 TCGA-XG-A823 
       71.05        78.21        10.16       103.17        20.19 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.79              0.10 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           137.59            316.73 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            15.58             23.77 
[1] "0.8 - 137.6 (15.6)" "0.1 - 316.7 (23.8)"
[1] "hr=" "2.1"
D40V2, continuous
D40V3, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    5  8
  2Q LOSS WILD-TYPE 83 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    8
  2Q LOSS WILD-TYPE   83   66
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               5                83
  MALE                 8                66
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     1
  2Q LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           1    11
  2Q LOSS WILD-TYPE                        18   123
D40V4, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         11               123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = 3P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED   60  2
  3P LOSS WILD-TYPE 96  4
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               62               100 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                 4 
$`3P LOSS MUTATED`
TCGA-P8-A6RX TCGA-PR-A5PF TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6GZ 
       17.75        17.95       137.59        58.88         1.05        30.51 
TCGA-QR-A6H5 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A70D TCGA-QR-A70J TCGA-QR-A70N 
       31.53        32.15         1.28         0.23        13.12         1.41 
TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK 
      117.14        14.20        12.39        17.95        36.23         6.94 
TCGA-QT-A5XL TCGA-QT-A5XN TCGA-QT-A5XP TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RW-A67W 
        1.81        25.18         4.41       108.26        50.63        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
        2.93         7.10        33.30         1.22        11.70        13.05 
TCGA-RW-A68C TCGA-RW-A7CZ TCGA-S7-A7WL TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
        6.28         4.41        31.59        31.04        26.96        40.70 
TCGA-S7-A7WT TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI 
       37.58        12.66        18.94       109.25        67.50       110.04 
TCGA-SQ-A6I6 TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-TT-A6YK TCGA-TT-A6YP 
        0.10       106.75       110.53       121.05        25.15        25.32 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HF TCGA-W2-A7UY TCGA-WB-A80P 
       14.20        17.16         1.18        17.69        10.65       316.73 
TCGA-WB-A80V TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A819 TCGA-WB-A81W TCGA-WB-A820 
       29.16        32.88         5.98        33.90        78.21        10.16 
TCGA-WB-A821 TCGA-XG-A823 
       93.11        20.19 

$`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        28.08 
TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GX TCGA-QR-A6H0 TCGA-QR-A6H1 
       35.01        23.11         1.25        19.04         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H6 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E 
        9.93        14.27        15.58         4.11       116.19         6.31 
TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70K TCGA-QR-A70W TCGA-QR-A70X 
        2.33        26.83        29.92         9.01        41.79         6.02 
TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        0.72         2.30         0.79        13.08        77.98         0.92 
TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        8.09        86.89        23.80         1.05         0.85        13.32 
TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7D0 TCGA-RW-A8AZ 
        7.96        72.79        15.02        41.88         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WU TCGA-S7-A7WV 
       20.09        30.21        37.25        35.51        30.51        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QF 
       20.58        25.32        18.08         9.73       114.77        82.62 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
       15.52       111.25         1.41        51.22        68.61        81.93 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YN 
        3.12        24.66        19.76        49.61         4.34        19.92 
TCGA-TT-A6YO TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       13.32        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 
       34.82        34.26         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        41.23        32.61        34.03        24.16        35.84 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        57.11        38.76        42.54        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       40.04        45.83        53.69        12.99        24.82         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A822 
       23.77        18.28        71.05       103.17 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.10              0.72 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           316.73            127.56 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           20.025            22.715 
[1] "0.1 - 316.7 (20.0)" "0.7 - 127.6 (22.7)"
[1] "hr=" "1.8"
D41V2, continuous
D41V3, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   38 24
  3P LOSS WILD-TYPE 50 50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     38   24
  3P LOSS WILD-TYPE   50   50
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              38                50
  MALE                24                50
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  1     0
  3P LOSS WILD-TYPE                                0     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                          10    50
  3P LOSS WILD-TYPE                         9    84
D41V4, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                     10                 9
  WHITE                                         50                84
[1] 4 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 = 3Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED   86  2
  3Q LOSS WILD-TYPE 70  4
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               88                74 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                 4 
$`3Q LOSS MUTATED`
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-QR-A6GO TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GZ 
        2.27        17.75        35.01       137.59        58.88        30.51 
TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 
        9.21        14.17        31.53        15.58        32.15         1.28 
TCGA-QR-A70D TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A7IN 
        0.23        13.12         1.41        14.20        41.79        12.39 
TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XP 
       17.95        36.23         6.94         0.72        25.18         4.41 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 
      108.26        50.63        19.86         2.93         7.10        33.30 
TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
        0.85         1.22        11.70        13.05         7.96         6.28 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-S7-A7WL TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
        4.41         1.78        31.59        31.04        26.96        40.70 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       12.66        18.94        18.08       109.25        82.62        67.50 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
      110.04        15.52       111.25         1.41         0.10        51.22 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
      106.75       110.53       121.05         3.12        24.66        19.76 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
        4.34        25.15        25.32        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HF TCGA-W2-A7UY TCGA-WB-A80M 
       19.86        12.03        12.49        17.69        10.65         4.47 
TCGA-WB-A80N TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A818 
        4.73       316.73        29.16        32.88        41.23        34.03 
TCGA-WB-A819 TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81W 
       33.90        57.11        38.76         1.61        18.28        78.21 
TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       10.16        93.11       103.17        20.19 

$`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        17.95        81.70        28.08 
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H2 TCGA-QR-A6H3 
       23.11         1.25        19.04         1.05         9.93        14.27 
TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
        4.11       116.19         6.31         2.33        26.83        29.92 
TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70X TCGA-QT-A5XL TCGA-QT-A5XO TCGA-QT-A69Q 
        9.01       117.14         6.02         1.81         2.30         0.79 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A681 
       13.08        77.98         0.92         8.09        86.89        23.80 
TCGA-RW-A684 TCGA-RW-A686 TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A8AZ 
        1.05        13.32        72.79        15.02        41.88         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WT TCGA-S7-A7WU 
       20.09        30.21        37.25        35.51        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SR-A6MQ 
       27.91        20.58        25.32         9.73       114.77        68.61 
TCGA-SR-A6MS TCGA-SR-A6N0 TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7HE TCGA-W2-A7HH 
       81.93        49.61        19.92        13.32        16.60        25.61 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80O TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A815 
       34.82        34.26         4.21       127.56        19.59         5.98 
TCGA-WB-A817 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81H TCGA-WB-A81I 
       32.61        24.16        35.84        37.18        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       24.36        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81S TCGA-WB-A81V 
       23.77        71.05 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.10              0.79 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           316.73            127.56 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            18.61             24.26 
[1] "0.1 - 316.7 (18.6)" "0.8 - 127.6 (24.3)"
[1] "hr=" "2.3"
D42V2, continuous
D42V3, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   47 41
  3Q LOSS WILD-TYPE 41 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     47   41
  3Q LOSS WILD-TYPE   41   33
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              47                41
  MALE                41                33
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  1     2
  3Q LOSS WILD-TYPE                                0     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                          10    72
  3Q LOSS WILD-TYPE                         9    62
D42V4, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                 3
  BLACK OR AFRICAN AMERICAN                     10                 9
  WHITE                                         72                62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = 4P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    11   0
  4P LOSS WILD-TYPE 145   6
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               11               151 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                0                 6 
$`4P LOSS MUTATED`
TCGA-QR-A6GS TCGA-QR-A700 TCGA-QR-A706 TCGA-QR-A70N TCGA-QT-A69Q TCGA-RT-A6YA 
        1.25        32.15         4.11         1.41         0.79        50.63 
TCGA-RW-A67X TCGA-RW-A68C TCGA-TT-A6YP TCGA-WB-A81J TCGA-WB-A821 
        2.93         6.28        25.32        24.36        93.11 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GT TCGA-QR-A6GU 
       81.70        28.08        35.01        23.11       137.59        58.88 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       19.04         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A70C TCGA-QR-A70D 
       14.27        31.53        15.58         1.28       116.19         0.23 
TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K 
        6.31         2.33        26.83        29.92        13.12         9.01 
TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
      117.14        14.20        41.79         6.02        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       36.23         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC 
        4.41        13.08        77.98         0.92       108.26         8.09 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       86.89        19.86         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-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02        41.88         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        30.21        37.25        35.51        31.04 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       26.96        40.70        37.58        30.51        27.91        20.58 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       25.32        12.66        18.94        18.08         9.73       114.77 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      109.25        82.62        67.50       110.04        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT 
        1.41         0.10        51.22        68.61        81.93       106.75 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
      110.53       121.05         3.12        24.66        19.76        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7H5 TCGA-W2-A7H7 
        4.34        25.15        19.92        13.32        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        34.82        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       316.73       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        41.23        32.61        34.03        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       40.04        45.83        53.69        12.99        24.82         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A822 
       23.77        18.28        71.05        78.21        10.16       103.17 
TCGA-XG-A823 
       20.19 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.79              0.10 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            93.11            316.73 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             6.28             22.32 
[1] "0.8 - 93.1 (6.3)"   "0.1 - 316.7 (22.3)"
[1] "hr="     "2.6e+07"
D43V2, continuous
D43V3, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    5  6
  4P LOSS WILD-TYPE 83 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      5    6
  4P LOSS WILD-TYPE   83   68
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               5                83
  MALE                 6                68
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     0
  4P LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                           1    10
  4P LOSS WILD-TYPE                        18   124
D43V4, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         10               124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = 4Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    10   0
  4Q LOSS WILD-TYPE 146   6
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10               152 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                0                 6 
$`4Q LOSS MUTATED`
TCGA-QR-A700 TCGA-QR-A70N TCGA-QT-A69Q TCGA-RT-A6YA TCGA-RW-A67W TCGA-RW-A67X 
       32.15         1.41         0.79        50.63        19.86         2.93 
TCGA-RW-A68C TCGA-TT-A6YP TCGA-WB-A81J TCGA-WB-A821 
        6.28        25.32        24.36        93.11 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 
        9.93        14.27        31.53        15.58         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
      116.19         0.23         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
       13.12         9.01       117.14        14.20        41.79         6.02 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       12.39        17.95        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        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 
      108.26         8.09        86.89         7.10        33.30        23.80 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
        1.05         0.85        13.32         1.22        11.70        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        41.88         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89        20.09        31.59        30.21        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       31.04        26.96        40.70        37.58        30.51        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 
       20.58        25.32        12.66        18.94        18.08         9.73 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      114.77       109.25        82.62        67.50       110.04        15.52 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
      111.25         1.41         0.10        51.22        68.61        81.93 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
      106.75       110.53       121.05         3.12        24.66        19.76 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7H5 
       49.61         4.34        25.15        19.92        13.32        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        34.82        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       316.73       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        41.23        32.61        34.03        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       24.16        35.84        37.18        57.11        38.76        42.54 
TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       22.32        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
        1.61        23.77        18.28        71.05        78.21        10.16 
TCGA-WB-A822 TCGA-XG-A823 
      103.17        20.19 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.79              0.10 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            93.11            316.73 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            22.11             21.45 
[1] "0.8 - 93.1 (22.1)"  "0.1 - 316.7 (21.4)"
[1] "hr="     "2.6e+07"
D44V2, continuous
D44V3, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    4  6
  4Q LOSS WILD-TYPE 84 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4    6
  4Q LOSS WILD-TYPE   84   68
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               4                84
  MALE                 6                68
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0     0
  4Q LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                           1     9
  4Q LOSS WILD-TYPE                        18   125
D44V4, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          9               125
[1] 4 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 = 5P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     5   0
  5P LOSS WILD-TYPE 151   6
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                5               157 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                0                 6 
$`5P LOSS MUTATED`
TCGA-QR-A7IN TCGA-QT-A69Q TCGA-RW-A68C TCGA-W2-A7H7 TCGA-W2-A7UY 
       12.39         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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 
        9.93        14.27        31.53        15.58        32.15         1.28 
TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        4.11       116.19         0.23         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R 
       29.92        13.12         9.01         1.41       117.14        14.20 
TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       41.79         6.02        17.95        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        13.08        77.98 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92       108.26        50.63         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        41.88         4.41         1.78         2.89        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       31.59        30.21        37.25        35.51        31.04        26.96 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       40.70        37.58        30.51        27.91        20.58        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       12.66        18.94        18.08         9.73       114.77       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       82.62        67.50       110.04        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
        0.10        51.22        68.61        81.93       106.75       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      121.05         3.12        24.66        19.76        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HA 
       25.15        19.92        13.32        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-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       34.82        34.26         4.47         4.73         4.21       316.73 
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        41.23 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        34.03        33.90        24.16        35.84        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       57.11        38.76        42.54        22.32        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       45.83        53.69        12.99        24.82         1.61        23.77 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 
       18.28        71.05        78.21        10.16        93.11       103.17 
TCGA-XG-A823 
       20.19 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.79              0.10 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            17.16            316.73 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            10.65             23.77 
[1] "0.8 - 17.2 (10.7)"  "0.1 - 316.7 (23.8)"
[1] "hr="     "9300000"
D45V2, continuous
D45V3, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    2  3
  5P LOSS WILD-TYPE 86 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    3
  5P LOSS WILD-TYPE   86   71
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               2                86
  MALE                 3                71
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     0
  5P LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           1     4
  5P LOSS WILD-TYPE                        18   130
D45V4, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          4               130
[1] 4 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 = 5Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED     7   0
  5Q LOSS WILD-TYPE 149   6
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7               155 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                0                 6 
$`5Q LOSS MUTATED`
TCGA-QR-A7IN TCGA-QT-A5XJ TCGA-QT-A69Q TCGA-RW-A67Y TCGA-RW-A68C TCGA-WB-A80M 
       12.39        36.23         0.79         7.10         6.28         4.47 
TCGA-WB-A81W 
       78.21 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 
        9.93        14.27        31.53        15.58        32.15         1.28 
TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        4.11       116.19         0.23         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R 
       29.92        13.12         9.01         1.41       117.14        14.20 
TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IP TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       41.79         6.02        17.95         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        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
      108.26        50.63         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        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89        20.09        31.59        30.21 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       37.25        35.51        31.04        26.96        40.70        37.58 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 
       30.51        27.91        20.58        25.32        12.66        18.94 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       18.08         9.73       114.77       109.25        82.62        67.50 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
      110.04        15.52       111.25         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX 
       68.61        81.93       106.75       110.53       121.05         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        19.76        49.61         4.34        25.15        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
       13.32        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-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       34.82        34.26         4.73         4.21       316.73       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        41.23        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       34.03        33.90        24.16        35.84        37.18        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        42.54        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       53.69        12.99        24.82         1.61        23.77        18.28 
TCGA-WB-A81V TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        10.16        93.11       103.17        20.19 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.79              0.10 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            78.21            316.73 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             7.10             23.11 
[1] "0.8 - 78.2 (7.1)"   "0.1 - 316.7 (23.1)"
[1] "hr="     "2.6e+07"
D46V2, continuous
D46V3, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    3  4
  5Q LOSS WILD-TYPE 85 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3    4
  5Q LOSS WILD-TYPE   85   70
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               3                85
  MALE                 4                70
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  0     0
  5Q LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                           2     5
  5Q LOSS WILD-TYPE                        17   129
D46V4, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          5               129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = 6Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    18   1
  6Q LOSS WILD-TYPE 138   5
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               19               143 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                1                 5 
$`6Q LOSS MUTATED`
TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QR-A70W TCGA-QT-A5XN TCGA-S7-A7WM 
        2.27        81.70        35.01        41.79        25.18        30.21 
TCGA-S7-A7WN TCGA-S7-A7WR TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-W2-A7HC TCGA-W2-A7UY 
       37.25        40.70        24.66         4.34        12.03        10.65 
TCGA-WB-A80O TCGA-WB-A80V TCGA-WB-A819 TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A820 
        4.21        29.16        33.90         1.61        23.77        10.16 
TCGA-XG-A823 
       20.19 

$`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        17.75         5.88        17.95        28.08 
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY 
       23.11         1.25       137.59        58.88        19.04         1.05 
TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
       30.51         9.21        14.17         9.93        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D 
       15.58        32.15         1.28         4.11       116.19         0.23 
TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K 
        6.31         2.33        26.83        29.92        13.12         9.01 
TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
        1.41       117.14        14.20         6.02        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A5XP 
       36.23         6.94         1.81         0.72         2.30         4.41 
TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA 
        0.79        13.08        77.98         0.92       108.26        50.63 
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-A688 TCGA-RW-A689 
       23.80         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        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WO 
        4.41         1.78         2.89        20.09        31.59        35.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       31.04        26.96        37.58        30.51        27.91        20.58 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       25.32        12.66        18.94        18.08         9.73       114.77 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      109.25        82.62        67.50       110.04        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT 
        1.41         0.10        51.22        68.61        81.93       106.75 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YK 
      110.53       121.05         3.12        19.76        49.61        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       19.92        13.32        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        34.82 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80Y 
       34.26         4.47         4.73       316.73       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        41.23        32.61        34.03        24.16 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       24.36        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       18.28        71.05        78.21        93.11       103.17 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             1.61              0.10 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            81.70            316.73 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            24.66             20.09 
[1] "1.6 - 81.7 (24.7)"  "0.1 - 316.7 (20.1)"
[1] "hr=" "1.8"
D47V2, continuous
D47V3, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   12  7
  6Q LOSS WILD-TYPE 76 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     12    7
  6Q LOSS WILD-TYPE   76   67
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              12                76
  MALE                 7                67
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0     0
  6Q LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           1    17
  6Q LOSS WILD-TYPE                        18   117
D47V4, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         17               117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = 7Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     5   1
  7Q LOSS WILD-TYPE 151   5
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6               156 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                 5 
$`7Q LOSS MUTATED`
TCGA-QR-A70H TCGA-QT-A5XK TCGA-SP-A6QF TCGA-SR-A6MQ TCGA-WB-A81N TCGA-WB-A820 
       26.83         6.94        82.62        68.61        53.69        10.16 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 
        9.93        14.27        31.53        15.58        32.15         1.28 
TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70I 
        4.11       116.19         0.23         6.31         2.33        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W 
       13.12         9.01         1.41       117.14        14.20        41.79 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A5XM 
        6.02        12.39        17.95        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        13.08        77.98 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92       108.26        50.63         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        41.88         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        30.21        37.25        35.51        31.04 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       26.96        40.70        37.58        30.51        27.91        20.58 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       25.32        12.66        18.94        18.08         9.73       114.77 
TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
      109.25        67.50       110.04        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
        0.10        51.22        81.93       106.75       110.53       121.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        19.76        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       19.92        13.32        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        34.82        34.26         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      316.73       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 
       41.23        32.61        34.03        33.90        24.16        35.84 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        57.11        38.76        42.54        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       40.04        45.83        12.99        24.82         1.61        23.77 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       18.28        71.05        78.21        93.11       103.17        20.19 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             6.94              0.10 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            82.62            316.73 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           40.260            20.385 
[1] "6.9 - 82.6 (40.3)"  "0.1 - 316.7 (20.4)"
[1] "hr=" "5.3"
D48V2, continuous
D48V3, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    3  3
  7Q LOSS WILD-TYPE 85 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    3
  7Q LOSS WILD-TYPE   85   71
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               3                85
  MALE                 3                71
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     2
  7Q LOSS WILD-TYPE                                1     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           1     3
  7Q LOSS WILD-TYPE                        18   131
D48V4, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 3
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                          3               131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = 8P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    18   2
  8P LOSS WILD-TYPE 138   4
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               20               142 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                 4 
$`8P LOSS MUTATED`
TCGA-PR-A5PF TCGA-PR-A5PG TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A700 TCGA-QR-A70K 
       17.95        81.70       137.59        19.04        32.15         9.01 
TCGA-RT-A6YA TCGA-RW-A68A TCGA-RW-A68D TCGA-S7-A7WR TCGA-S7-A7WT TCGA-SR-A6MT 
       50.63        13.05        72.79        40.70        37.58       106.75 
TCGA-W2-A7H5 TCGA-W2-A7HE TCGA-WB-A80V TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       14.20        16.60        29.16        12.99        24.82         1.61 
TCGA-WB-A81T TCGA-WB-A820 
       18.28        10.16 

$`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        17.75         5.88        28.08 
TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6GZ 
       35.01        23.11         1.25        58.88         1.05        30.51 
TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
        9.21        14.17         9.93        14.27        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G 
        1.28         4.11       116.19         0.23         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R 
       26.83        29.92        13.12         1.41       117.14        14.20 
TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK 
       41.79         6.02        12.39        17.95        36.23         6.94 
TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q 
        1.81         0.72        25.18         2.30         4.41         0.79 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V 
       13.08        77.98         0.92       108.26         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-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       15.02        41.88         4.41         1.78         2.89        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       31.59        30.21        37.25        35.51        31.04        26.96 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 
       30.51        27.91        20.58        25.32        12.66        18.94 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       18.08         9.73       114.77       109.25        82.62        67.50 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
      110.04        15.52       111.25         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY 
       68.61        81.93       110.53       121.05         3.12        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       19.76        49.61         4.34        25.15        19.92        13.32 
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-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       17.69        25.61        10.65        34.82        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A814 
        4.73         4.21       316.73       127.56        19.59        32.88 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A 
        5.98        41.23        32.61        34.03        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81S TCGA-WB-A81V 
       24.36        40.04        45.83        53.69        23.77        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       78.21        93.11       103.17        20.19 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             1.61              0.10 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           137.59            316.73 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            21.93             21.45 
[1] "1.6 - 137.6 (21.9)" "0.1 - 316.7 (21.4)"
[1] "hr=" "3"  
D49V2, continuous
D49V3, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   13  7
  8P LOSS WILD-TYPE 75 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     13    7
  8P LOSS WILD-TYPE   75   67
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              13                75
  MALE                 7                67
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  0     1
  8P LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                           1    18
  8P LOSS WILD-TYPE                        18   116
D49V4, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         18               116
[1] 4 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 = 8Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    11   1
  8Q LOSS WILD-TYPE 145   5
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               12               150 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                 5 
$`8Q LOSS MUTATED`
TCGA-QR-A6GX TCGA-QR-A700 TCGA-QR-A70K TCGA-RW-A68A TCGA-S7-A7WR TCGA-SR-A6MT 
       19.04        32.15         9.01        13.05        40.70       106.75 
TCGA-SR-A6MX TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HD TCGA-WB-A80K TCGA-WB-A80V 
        3.12        14.20        17.16        12.49        34.82        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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       58.88         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       14.27        31.53        15.58         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
        1.41       117.14        14.20        41.79         6.02        12.39 
TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
       17.95        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        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
      108.26        50.63         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 
       41.88         4.41         1.78         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WT 
       30.21        37.25        35.51        31.04        26.96        37.58 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 
       30.51        27.91        20.58        25.32        12.66        18.94 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       18.08         9.73       114.77       109.25        82.62        67.50 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
      110.04        15.52       111.25         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MY TCGA-SR-A6MZ 
       68.61        81.93       110.53       121.05        24.66        19.76 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15        19.92        13.32        25.32 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
        1.18        19.86        12.03        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        34.26         4.47         4.73         4.21       316.73 
TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 
      127.56        19.59        32.88         5.98        41.23        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       34.03        33.90        24.16        35.84        37.18        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        42.54        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       53.69        12.99        24.82         1.61        23.77        18.28 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        78.21        10.16        93.11       103.17        20.19 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             3.12              0.10 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           106.75            316.73 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           18.100            22.715 
[1] "3.1 - 106.8 (18.1)" "0.1 - 316.7 (22.7)"
[1] "hr=" "3.1"
D50V2, continuous
D50V3, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    7  5
  8Q LOSS WILD-TYPE 81 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      7    5
  8Q LOSS WILD-TYPE   81   69
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               7                81
  MALE                 5                69
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     0
  8Q LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           1    11
  8Q LOSS WILD-TYPE                        18   123
D50V4, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         11               123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = 9P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED     9   2
  9P LOSS WILD-TYPE 147   4
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               11               151 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                2                 4 
$`9P LOSS MUTATED`
TCGA-QR-A6GO TCGA-QR-A70R TCGA-QR-A7IP TCGA-QT-A5XP TCGA-RT-A6YA TCGA-SP-A6QJ 
       35.01        14.20        17.95         4.41        50.63        15.52 
TCGA-SR-A6MV TCGA-W2-A7H5 TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A820 
      121.05        14.20        24.82         1.61        10.16 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU 
       81.70        28.08        23.11         1.25       137.59        58.88 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       19.04         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 
       14.27        31.53        15.58        32.15         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
      116.19         0.23         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70W TCGA-QR-A70X 
       13.12         9.01         1.41       117.14        41.79         6.02 
TCGA-QR-A7IN TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
       12.39        36.23         6.94         1.81         0.72        25.18 
TCGA-QT-A5XO TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        2.30         0.79        13.08        77.98         0.92       108.26 
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-A688 TCGA-RW-A689 
       23.80         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        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89        20.09        31.59        30.21 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       37.25        35.51        31.04        26.96        40.70        37.58 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 
       30.51        27.91        20.58        25.32        12.66        18.94 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       18.08         9.73       114.77       109.25        82.62        67.50 
TCGA-SP-A6QI TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
      110.04       111.25         1.41         0.10        51.22        68.61 
TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
       81.93       106.75       110.53         3.12        24.66        19.76 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15        19.92        13.32        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        34.82        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       316.73       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        41.23        32.61        34.03        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       24.16        35.84        37.18        57.11        38.76        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       22.32        24.36        40.04        45.83        53.69        12.99 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       23.77        18.28        71.05        78.21        93.11       103.17 
TCGA-XG-A823 
       20.19 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             1.61              0.10 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           121.05            316.73 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            15.52             23.11 
[1] "1.6 - 121.0 (15.5)" "0.1 - 316.7 (23.1)"
[1] "hr=" "5.8"
D51V2, continuous
D51V3, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    6  5
  9P LOSS WILD-TYPE 82 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6    5
  9P LOSS WILD-TYPE   82   69
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               6                82
  MALE                 5                69
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0     0
  9P LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                           1    10
  9P LOSS WILD-TYPE                        18   124
D51V4, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                18
  WHITE                                         10               124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = 9Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    10   1
  9Q LOSS WILD-TYPE 146   5
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11               151 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                1                 5 
$`9Q LOSS MUTATED`
TCGA-QR-A6GO TCGA-QR-A70R TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XP TCGA-RT-A6YA 
       35.01        14.20        17.95        36.23         4.41        50.63 
TCGA-SR-A6MP TCGA-SR-A6MV TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-WB-A81Q 
       51.22       121.05        14.20        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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU 
       81.70        28.08        23.11         1.25       137.59        58.88 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       19.04         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 
       14.27        31.53        15.58        32.15         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
      116.19         0.23         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70W TCGA-QR-A70X 
       13.12         9.01         1.41       117.14        41.79         6.02 
TCGA-QR-A7IN TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       12.39         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC 
        0.79        13.08        77.98         0.92       108.26         8.09 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 
       86.89        19.86         2.93         7.10        33.30        23.80 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
        1.05         0.85        13.32         1.22        11.70        13.05 
TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
        7.96         6.28        72.79        15.02        41.88         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89        20.09        31.59        30.21        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       35.51        31.04        26.96        40.70        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       27.91        20.58        25.32        12.66        18.94        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
        9.73       114.77       109.25        82.62        67.50       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MS 
       15.52       111.25         1.41         0.10        68.61        81.93 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
      106.75       110.53         3.12        24.66        19.76        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HA 
        4.34        25.15        19.92        13.32        25.32         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        34.82        34.26         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      316.73       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 
       41.23        32.61        34.03        33.90        24.16        35.84 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        57.11        38.76        42.54        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S 
       40.04        45.83        53.69        12.99         1.61        23.77 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 
       18.28        71.05        78.21        10.16        93.11       103.17 
TCGA-XG-A823 
       20.19 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             4.41              0.10 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           121.05            316.73 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            24.82             20.58 
[1] "4.4 - 121.0 (24.8)" "0.1 - 316.7 (20.6)"
[1] "hr=" "1.9"
D52V2, continuous
D52V3, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    6  5
  9Q LOSS WILD-TYPE 82 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      6    5
  9Q LOSS WILD-TYPE   82   69
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               6                82
  MALE                 5                69
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     0
  9Q LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           2     9
  9Q LOSS WILD-TYPE                        17   125
D52V4, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      2                17
  WHITE                                          9               125
[1] 4 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 = 11P LOSS MUTATION ANALYSIS
D53V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    53   1
  11P LOSS WILD-TYPE 103   5
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                54                108 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                  5 
$`11P LOSS MUTATED`
TCGA-P8-A6RX TCGA-P8-A6RY TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H2 TCGA-QR-A6H5 
       17.75         5.88        58.88        30.51         9.93        31.53 
TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N 
       15.58         1.28         4.11        13.12         9.01         1.41 
TCGA-QR-A70R TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
       14.20        12.39        17.95        13.08        77.98         0.92 
TCGA-RT-A6YA TCGA-RW-A67X TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A68A TCGA-RW-A68C 
       50.63         2.93        23.80         1.05        13.05         6.28 
TCGA-RW-A68F TCGA-RW-A7CZ TCGA-RW-A8AZ TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WU 
       15.02         4.41         2.89        31.04        26.96        30.51 
TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-SP-A6QD TCGA-SR-A6MT TCGA-SR-A6MU 
       20.58        12.66        18.94       109.25       106.75       110.53 
TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7UY TCGA-WB-A80M 
       49.61        25.15        25.32        17.16        10.65         4.47 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81P 
        5.98        41.23        22.32        40.04        45.83        12.99 
TCGA-WB-A81S TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       23.77        71.05        78.21        93.11       103.17        20.19 

$`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        17.95        81.70        28.08 
TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GY 
       35.01        23.11         1.25       137.59        19.04         1.05 
TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H3 TCGA-QR-A700 TCGA-QR-A70C TCGA-QR-A70D 
        9.21        14.17        14.27        32.15       116.19         0.23 
TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70P TCGA-QR-A70W 
        6.31         2.33        26.83        29.92       117.14        41.79 
TCGA-QR-A70X TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
        6.02        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       108.26         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        41.88         1.78        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WR TCGA-S7-A7WT 
       31.59        30.21        37.25        35.51        40.70        37.58 
TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QF 
       27.91        25.32        18.08         9.73       114.77        82.62 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.50       110.04        15.52       111.25         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY 
       51.22        68.61        81.93       121.05         3.12        24.66 
TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7H5 TCGA-W2-A7HA 
       19.76         4.34        19.92        13.32        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-WB-A80K TCGA-WB-A80L TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       34.82        34.26         4.73         4.21       316.73       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
       29.16        19.59        32.88        32.61        34.03        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       24.16        35.84        37.18        57.11        38.76        42.54 
TCGA-WB-A81J TCGA-WB-A81N TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A820 
       24.36        53.69        24.82         1.61        18.28        10.16 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.92               0.10 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            110.53             316.73 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            18.445             24.510 
[1] "0.9 - 110.5 (18.4)" "0.1 - 316.7 (24.5)"
[1] "hr=" "1.9"
D53V2, continuous
D53V3, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   26 28
  11P LOSS WILD-TYPE 62 46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     26   28
  11P LOSS WILD-TYPE   62   46
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               26                 62
  MALE                 28                 46
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     1
  11P LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           4    48
  11P LOSS WILD-TYPE                        15    86
D53V4, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       4                 15
  WHITE                                          48                 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(54) Variable = 11Q LOSS MUTATION ANALYSIS
D54V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    39   1
  11Q LOSS WILD-TYPE 117   5
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                40                122 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                  5 
$`11Q LOSS MUTATED`
TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-QR-A6GS TCGA-QR-A6GU TCGA-QR-A6GZ 
       17.75         5.88        17.95         1.25        58.88        30.51 
TCGA-QR-A6H2 TCGA-QR-A6H5 TCGA-QR-A70N TCGA-QR-A7IN TCGA-QT-A5XL TCGA-QT-A5XO 
        9.93        31.53         1.41        12.39         1.81         2.30 
TCGA-QT-A69Q TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6YA TCGA-RW-A67X TCGA-RW-A681 
        0.79        77.98         0.92        50.63         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        31.04 
TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-SR-A6MT 
       26.96        30.51        20.58        12.66        18.94       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        23.77 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-XG-A823 
       71.05        78.21        93.11        20.19 

$`11Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO 
       31.46        29.03         2.27        81.70        28.08        35.01 
TCGA-QR-A6GR TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H1 
       23.11       137.59        19.04         1.05         9.21        14.17 
TCGA-QR-A6H3 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       14.27        15.58        32.15         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IP 
        9.01       117.14        14.20        41.79         6.02        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A7U0 
       36.23         6.94         0.72        25.18         4.41        13.08 
TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A680 
      108.26         8.09        86.89        19.86         7.10        33.30 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68A TCGA-RW-A68B 
        1.05         0.85        13.32         1.22        13.05         7.96 
TCGA-RW-A68D TCGA-RW-A68G TCGA-RW-A7D0 TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
       72.79        41.88         1.78        20.09        31.59        30.21 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WX 
       37.25        35.51        40.70        37.58        27.91        25.32 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       18.08         9.73       114.77       109.25        82.62        67.50 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
      110.04        15.52       111.25         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY 
       68.61        81.93       110.53       121.05         3.12        24.66 
TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7H5 
       19.76         4.34        25.15        19.92        13.32        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-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       17.69        25.61        34.82        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       316.73       127.56        29.16        19.59        32.88 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
       41.23        32.61        34.03        33.90        24.16        35.84 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        57.11        38.76        42.54        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T 
       40.04        45.83        53.69        24.82         1.61        18.28 
TCGA-WB-A820 TCGA-WB-A822 
       10.16       103.17 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.79               0.10 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            106.75             316.73 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             17.85              24.51 
[1] "0.8 - 106.8 (17.9)" "0.1 - 316.7 (24.5)"
[1] "hr=" "1.1"
D54V2, continuous
D54V3, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   21 19
  11Q LOSS WILD-TYPE 67 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     21   19
  11Q LOSS WILD-TYPE   67   55
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               21                 67
  MALE                 19                 55
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     1
  11Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           5    34
  11Q LOSS WILD-TYPE                        14   100
D54V4, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       5                 14
  WHITE                                          34                100
[1] 4 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 = 13Q LOSS MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED     8   0
  13Q LOSS WILD-TYPE 148   6
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 8                154 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 0                  6 
$`13Q LOSS MUTATED`
TCGA-PR-A5PF TCGA-QR-A700 TCGA-QR-A70R TCGA-QT-A5XP TCGA-RW-A68A TCGA-S7-A7WX 
       17.95        32.15        14.20         4.41        13.05        25.32 
TCGA-SP-A6QF TCGA-W2-A7H5 
       82.62        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        17.75         5.88        81.70 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU 
       28.08        35.01        23.11         1.25       137.59        58.88 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       19.04         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       14.27        31.53        15.58         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
        9.01         1.41       117.14        41.79         6.02        12.39 
TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
       17.95        36.23         6.94         1.81         0.72        25.18 
TCGA-QT-A5XO TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        2.30         0.79        13.08        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       50.63         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-A68D TCGA-RW-A68F TCGA-RW-A68G 
       11.70         7.96         6.28        72.79        15.02        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89        20.09        31.59        30.21 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       37.25        35.51        31.04        26.96        40.70        37.58 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       30.51        27.91        20.58        12.66        18.94        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
        9.73       114.77       109.25        67.50       110.04        15.52 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
      111.25         1.41         0.10        51.22        68.61        81.93 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
      106.75       110.53       121.05         3.12        24.66        19.76 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15        19.92        13.32        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        34.82        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       316.73       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        41.23        32.61        34.03        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       24.16        35.84        37.18        57.11        38.76        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       22.32        24.36        40.04        45.83        53.69        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        23.77        18.28        71.05        78.21 
TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       10.16        93.11       103.17        20.19 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              4.41               0.10 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             82.62             316.73 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            16.075             22.715 
[1] "4.4 - 82.6 (16.1)"  "0.1 - 316.7 (22.7)"
[1] "hr="     "2.6e+07"
D55V2, continuous
D55V3, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    4  4
  13Q LOSS WILD-TYPE 84 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4    4
  13Q LOSS WILD-TYPE   84   70
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                4                 84
  MALE                  4                 70
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  0     1
  13Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                           1     6
  13Q LOSS WILD-TYPE                        18   128
D55V4, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           6                128
[1] 4 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 = 14Q LOSS MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    20   0
  14Q LOSS WILD-TYPE 136   6
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                20                142 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 0                  6 
$`14Q LOSS MUTATED`
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A70H TCGA-QR-A70R TCGA-QR-A7IP TCGA-QT-A69Q 
       28.08        35.01        26.83        14.20        17.95         0.79 
TCGA-RT-A6YA TCGA-RW-A67X TCGA-RW-A689 TCGA-RW-A68C TCGA-S7-A7WR TCGA-S7-A7WV 
       50.63         2.93        11.70         6.28        40.70        27.91 
TCGA-SR-A6MS TCGA-SR-A6MV TCGA-W2-A7H5 TCGA-W2-A7HF TCGA-WB-A815 TCGA-WB-A81K 
       81.93       121.05        14.20        17.69         5.98        40.04 
TCGA-WB-A81S TCGA-WB-A821 
       23.77        93.11 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GX 
       81.70        23.11         1.25       137.59        58.88        19.04 
TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
        1.05        30.51         9.21        14.17         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       31.53        15.58        32.15         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K 
        0.23         6.31         2.33        29.92        13.12         9.01 
TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QT-A5XJ 
        1.41       117.14        41.79         6.02        12.39        36.23 
TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP 
        6.94         1.81         0.72        25.18         2.30         4.41 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V 
       13.08        77.98         0.92       108.26         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 
       19.86         7.10        33.30        23.80         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A68F 
       13.32         1.22        13.05         7.96        72.79        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
       41.88         4.41         1.78         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WT 
       30.21        37.25        35.51        31.04        26.96        37.58 
TCGA-S7-A7WU TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       30.51        20.58        25.32        12.66        18.94        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
        9.73       114.77       109.25        82.62        67.50       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       15.52       111.25         1.41         0.10        51.22        68.61 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
      106.75       110.53         3.12        24.66        19.76        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 
        4.34        25.15        19.92        13.32        25.32        17.16 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
        1.18        19.86        12.03        12.49        16.60        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       10.65        34.82        34.26         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A816 
      316.73       127.56        29.16        19.59        32.88        41.23 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        34.03        33.90        24.16        35.84        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81M 
       57.11        38.76        42.54        22.32        24.36        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V 
       53.69        12.99        24.82         1.61        18.28        71.05 
TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A822 TCGA-XG-A823 
       78.21        10.16       103.17        20.19 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.79               0.10 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            121.05             316.73 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            25.300             20.385 
[1] "0.8 - 121.0 (25.3)" "0.1 - 316.7 (20.4)"
[1] "hr="     "8.5e+07"
D56V2, continuous
D56V3, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   10 10
  14Q LOSS WILD-TYPE 78 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     10   10
  14Q LOSS WILD-TYPE   78   64
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               10                 78
  MALE                 10                 64
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0     0
  14Q LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                           1    19
  14Q LOSS WILD-TYPE                        18   115
D56V4, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                          19                115
[1] 4 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 = 15Q LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED     3   0
  15Q LOSS WILD-TYPE 153   6
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 3                159 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 0                  6 
$`15Q LOSS MUTATED`
TCGA-SR-A6MQ TCGA-SR-A6MV TCGA-W2-A7HF 
       68.61       121.05        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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 
        9.93        14.27        31.53        15.58        32.15         1.28 
TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        4.11       116.19         0.23         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R 
       29.92        13.12         9.01         1.41       117.14        14.20 
TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK 
       41.79         6.02        12.39        17.95        36.23         6.94 
TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q 
        1.81         0.72        25.18         2.30         4.41         0.79 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC 
       13.08        77.98         0.92       108.26        50.63         8.09 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 
       86.89        19.86         2.93         7.10        33.30        23.80 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
        1.05         0.85        13.32         1.22        11.70        13.05 
TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
        7.96         6.28        72.79        15.02        41.88         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89        20.09        31.59        30.21        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       35.51        31.04        26.96        40.70        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       27.91        20.58        25.32        12.66        18.94        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
        9.73       114.77       109.25        82.62        67.50       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MS 
       15.52       111.25         1.41         0.10        51.22        81.93 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
      106.75       110.53         3.12        24.66        19.76        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        25.15        19.92        13.32        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-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        10.65        34.82        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       316.73       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        41.23        32.61        34.03        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       24.36        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
        1.61        23.77        18.28        71.05        78.21        10.16 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       93.11       103.17        20.19 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             17.69               0.10 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            121.05             316.73 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             68.61              20.58 
[1] "17.7 - 121.0 (68.6)" "0.1 - 316.7 (20.6)" 
[1] "hr="     "3.1e+07"
D57V2, continuous
D57V3, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    3  0
  15Q LOSS WILD-TYPE 85 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3    0
  15Q LOSS WILD-TYPE   85   74
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                3                 85
  MALE                  0                 74
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0     1
  15Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           1     1
  15Q LOSS WILD-TYPE                        18   133
D57V4, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           1                133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = 16P LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     6   3
  16P LOSS WILD-TYPE 150   3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                153 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                  3 
$`16P LOSS MUTATED`
TCGA-PR-A5PF TCGA-QR-A700 TCGA-QR-A70K TCGA-QR-A70P TCGA-QT-A69Q TCGA-SR-A6MT 
       17.95        32.15         9.01       117.14         0.79       106.75 
TCGA-SR-A6MX TCGA-WB-A81Q TCGA-WB-A81S 
        3.12        24.82        23.77 

$`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        17.75         5.88        81.70 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU 
       28.08        35.01        23.11         1.25       137.59        58.88 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       19.04         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       14.27        31.53        15.58         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
        1.41        14.20        41.79         6.02        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       36.23         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA 
        4.41        13.08        77.98         0.92       108.26        50.63 
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-A688 TCGA-RW-A689 
       23.80         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        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89        20.09        31.59        30.21 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       37.25        35.51        31.04        26.96        40.70        37.58 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 
       30.51        27.91        20.58        25.32        12.66        18.94 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       18.08         9.73       114.77       109.25        82.62        67.50 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
      110.04        15.52       111.25         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MY TCGA-SR-A6MZ 
       68.61        81.93       110.53       121.05        24.66        19.76 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15        19.92        13.32        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        34.82        34.26 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       316.73       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        41.23        32.61        34.03 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
       33.90        24.16        35.84        37.18        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54        22.32        24.36        40.04        45.83        53.69 
TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
       12.99         1.61        18.28        71.05        78.21        10.16 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       93.11       103.17        20.19 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.79               0.10 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            117.14             316.73 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             23.77              20.58 
[1] "0.8 - 117.1 (23.8)" "0.1 - 316.7 (20.6)"
[1] "hr=" "14" 
D58V2, continuous
D58V3, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    4  5
  16P LOSS WILD-TYPE 84 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4    5
  16P LOSS WILD-TYPE   84   69
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                4                 84
  MALE                  5                 69
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     0
  16P LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           0     9
  16P LOSS WILD-TYPE                        19   125
D58V4, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           9                125
[1] 4 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 = 16Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED     5   0
  16Q LOSS WILD-TYPE 151   6
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                157 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 0                  6 
$`16Q LOSS MUTATED`
TCGA-PR-A5PF TCGA-QR-A700 TCGA-QT-A69Q TCGA-SR-A6MT TCGA-WB-A81S 
       17.95        32.15         0.79       106.75        23.77 

$`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        17.75         5.88        81.70 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU 
       28.08        35.01        23.11         1.25       137.59        58.88 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       19.04         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       14.27        31.53        15.58         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
        9.01         1.41       117.14        14.20        41.79         6.02 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       12.39        17.95        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        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
      108.26        50.63         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        41.88         4.41         1.78         2.89        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       31.59        30.21        37.25        35.51        31.04        26.96 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       40.70        37.58        30.51        27.91        20.58        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       12.66        18.94        18.08         9.73       114.77       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       82.62        67.50       110.04        15.52       111.25         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV 
        0.10        51.22        68.61        81.93       110.53       121.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        19.76        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       19.92        13.32        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        34.82        34.26         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      316.73       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 
       41.23        32.61        34.03        33.90        24.16        35.84 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        57.11        38.76        42.54        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       40.04        45.83        53.69        12.99        24.82         1.61 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 
       18.28        71.05        78.21        10.16        93.11       103.17 
TCGA-XG-A823 
       20.19 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.79               0.10 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            106.75             316.73 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             23.77              20.58 
[1] "0.8 - 106.8 (23.8)" "0.1 - 316.7 (20.6)"
[1] "hr="     "2.5e+07"
D59V2, continuous
D59V3, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    3  2
  16Q LOSS WILD-TYPE 85 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    2
  16Q LOSS WILD-TYPE   85   72
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                3                 85
  MALE                  2                 72
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     0
  16Q LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           0     5
  16Q LOSS WILD-TYPE                        19   129
D59V4, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           5                129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = 17P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   59  2
  17P LOSS WILD-TYPE 97  4
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                61                101 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                  4 
$`17P LOSS MUTATED`
TCGA-PR-A5PG TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6H1 
       81.70        23.11         1.25        58.88         1.05        14.17 
TCGA-QR-A6H2 TCGA-QR-A702 TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70R TCGA-QR-A70W 
        9.93         1.28        29.92        13.12        14.20        41.79 
TCGA-QR-A70X TCGA-QT-A5XN TCGA-QT-A69Q TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A681 
        6.02        25.18         0.79         2.93         7.10        23.80 
TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68C TCGA-RW-A68F 
        0.85         1.22        11.70        13.05         6.28        15.02 
TCGA-RW-A68G TCGA-RW-A7D0 TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WQ TCGA-S7-A7WT 
       41.88         1.78        31.59        30.21        26.96        37.58 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QD TCGA-SP-A6QJ 
       20.58        25.32        18.94        18.08       109.25        15.52 
TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MT TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
        0.10        68.61       106.75         4.34        25.15        19.92 
TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7UY TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
        1.18        12.03        10.65         4.73         4.21       316.73 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A818 TCGA-WB-A81J TCGA-WB-A81M 
       29.16        19.59         5.98        34.03        24.36        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81W 
       53.69        12.99        24.82        23.77        18.28        78.21 
TCGA-WB-A822 
      103.17 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GZ TCGA-QR-A6H0 
       28.08        35.01       137.59        19.04        30.51         9.21 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A706 TCGA-QR-A70C 
       14.27        31.53        15.58        32.15         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70K TCGA-QR-A70N 
        0.23         6.31         2.33        26.83         9.01         1.41 
TCGA-QR-A70P TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
      117.14        12.39        17.95        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        0.72         2.30         4.41        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A680 
      108.26        50.63         8.09        86.89        19.86        33.30 
TCGA-RW-A684 TCGA-RW-A686 TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A7CZ TCGA-RW-A8AZ 
        1.05        13.32         7.96        72.79         4.41         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WU 
       20.09        37.25        35.51        31.04        40.70        30.51 
TCGA-S7-A7WV TCGA-S7-A7X0 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QG 
       27.91        12.66         9.73       114.77        82.62        67.50 
TCGA-SP-A6QI TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MS TCGA-SR-A6MU 
      110.04       111.25         1.41        51.22        81.93       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YO 
      121.05         3.12        24.66        19.76        49.61        13.32 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HB TCGA-W2-A7HD TCGA-W2-A7HE 
       25.32        14.20        17.16        19.86        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80Q 
       17.69        25.61        34.82        34.26         4.47       127.56 
TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
       32.88        41.23        32.61        33.90        24.16        35.84 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81K 
       37.18        57.11        38.76        42.54        22.32        40.04 
TCGA-WB-A81R TCGA-WB-A81V TCGA-WB-A820 TCGA-WB-A821 TCGA-XG-A823 
        1.61        71.05        10.16        93.11        20.19 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.10               0.23 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            316.73             137.59 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             18.94              25.32 
[1] "0.1 - 316.7 (18.9)" "0.2 - 137.6 (25.3)"
[1] "hr=" "1"  
D60V2, continuous
D60V3, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   30 31
  17P LOSS WILD-TYPE 58 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     30   31
  17P LOSS WILD-TYPE   58   43
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               30                 58
  MALE                 31                 43
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  1     2
  17P LOSS WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                           3    53
  17P LOSS WILD-TYPE                        16    81
D60V4, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                       3                 16
  WHITE                                          53                 81
[1] 4 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 = 17Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    17   2
  17Q LOSS WILD-TYPE 139   4
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                19                143 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                  4 
$`17Q LOSS MUTATED`
TCGA-QR-A6GS TCGA-QR-A700 TCGA-QR-A70J TCGA-QT-A5XN TCGA-QT-A69Q TCGA-RT-A6YA 
        1.25        32.15        13.12        25.18         0.79        50.63 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A688 TCGA-RW-A68C TCGA-S7-A7WM TCGA-S7-A7WQ 
        2.93         7.10         1.22         6.28        30.21        26.96 
TCGA-S7-A7X1 TCGA-SQ-A6I6 TCGA-SR-A6MT TCGA-WB-A80P TCGA-WB-A81N TCGA-WB-A81Q 
       18.94         0.10       106.75       316.73        53.69        24.82 
TCGA-WB-A820 
       10.16 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GT TCGA-QR-A6GU 
       81.70        28.08        35.01        23.11       137.59        58.88 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       19.04         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       14.27        31.53        15.58         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70K 
        0.23         6.31         2.33        26.83        29.92         9.01 
TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
        1.41       117.14        14.20        41.79         6.02        12.39 
TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XO 
       17.95        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-A6YC 
        4.41        13.08        77.98         0.92       108.26         8.09 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 
       86.89        19.86        33.30        23.80         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A68F 
       13.32        11.70        13.05         7.96        72.79        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
       41.88         4.41         1.78         2.89        20.09        31.59 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       37.25        35.51        31.04        40.70        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 
       27.91        20.58        25.32        12.66        18.08         9.73 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      114.77       109.25        82.62        67.50       110.04        15.52 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU 
      111.25         1.41        51.22        68.61        81.93       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      121.05         3.12        24.66        19.76        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       25.15        19.92        13.32        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        34.82        34.26         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 
       41.23        32.61        34.03        33.90        24.16        35.84 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        57.11        38.76        42.54        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       40.04        45.83        12.99         1.61        23.77        18.28 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        78.21        93.11       103.17        20.19 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.10               0.23 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            316.73             137.59 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             18.94              22.32 
[1] "0.1 - 316.7 (18.9)" "0.2 - 137.6 (22.3)"
[1] "hr=" "3.7"
D61V2, continuous
D61V3, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    8 11
  17Q LOSS WILD-TYPE 80 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      8   11
  17Q LOSS WILD-TYPE   80   63
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                8                 80
  MALE                 11                 63
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  0     0
  17Q LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           1    18
  17Q LOSS WILD-TYPE                        18   116
D61V4, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                          18                116
[1] 4 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 = 18P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    16   0
  18P LOSS WILD-TYPE 140   6
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                16                146 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 0                  6 
$`18P LOSS MUTATED`
TCGA-P8-A5KD TCGA-QR-A6GY TCGA-QR-A6H2 TCGA-QR-A6H6 TCGA-QR-A70C TCGA-QR-A70I 
        2.27         1.05         9.93        15.58       116.19        29.92 
TCGA-QR-A7IP TCGA-RW-A67X TCGA-RW-A68G TCGA-S7-A7X2 TCGA-SP-A6QF TCGA-W2-A7H7 
       17.95         2.93        41.88        18.08        82.62        17.16 
TCGA-WB-A80O TCGA-WB-A819 TCGA-WB-A81W TCGA-WB-A821 
        4.21        33.90        78.21        93.11 

$`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        17.75         5.88        17.95        81.70 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU 
       28.08        35.01        23.11         1.25       137.59        58.88 
TCGA-QR-A6GX TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H3 TCGA-QR-A6H5 
       19.04        30.51         9.21        14.17        14.27        31.53 
TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G 
       32.15         1.28         4.11         0.23         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R 
       26.83        13.12         9.01         1.41       117.14        14.20 
TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       41.79         6.02        12.39        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        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       77.98         0.92       108.26        50.63         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 
       19.86         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-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       72.79        15.02         4.41         1.78         2.89        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       31.59        30.21        37.25        35.51        31.04        26.96 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       40.70        37.58        30.51        27.91        20.58        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG 
       12.66        18.94         9.73       114.77       109.25        67.50 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
      110.04        15.52       111.25         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX 
       68.61        81.93       106.75       110.53       121.05         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        19.76        49.61         4.34        25.15        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC 
       13.32        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        34.82 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
       34.26         4.47         4.73       316.73       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        41.23        32.61        34.03 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       24.16        35.84        37.18        57.11        38.76        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       22.32        24.36        40.04        45.83        53.69        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A820 
       24.82         1.61        23.77        18.28        71.05        10.16 
TCGA-WB-A822 TCGA-XG-A823 
      103.17        20.19 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              1.05               0.10 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            116.19             316.73 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            18.015             22.715 
[1] "1.1 - 116.2 (18.0)" "0.1 - 316.7 (22.7)"
[1] "hr="     "7.7e+07"
D62V2, continuous
D62V3, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    6 10
  18P LOSS WILD-TYPE 82 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      6   10
  18P LOSS WILD-TYPE   82   64
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                6                 82
  MALE                 10                 64
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0     2
  18P LOSS WILD-TYPE                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                           2    12
  18P LOSS WILD-TYPE                        17   122
D62V4, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                       2                 17
  WHITE                                          12                122
[1] 4 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 = 18Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED     6   0
  18Q LOSS WILD-TYPE 150   6
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 6                156 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 0                  6 
$`18Q LOSS MUTATED`
TCGA-QR-A6H2 TCGA-QR-A6H6 TCGA-QR-A7IP TCGA-QT-A5XO TCGA-WB-A819 TCGA-WB-A821 
        9.93        15.58        17.95         2.30        33.90        93.11 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
       14.27        31.53        32.15         1.28         4.11       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
        9.01         1.41       117.14        14.20        41.79         6.02 
TCGA-QR-A7IN TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
       12.39        36.23         6.94         1.81         0.72        25.18 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        4.41         0.79        13.08        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       50.63         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 
       41.88         4.41         1.78         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       30.21        37.25        35.51        31.04        26.96        40.70 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       37.58        30.51        27.91        20.58        25.32        12.66 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       18.94        18.08         9.73       114.77       109.25        82.62 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.50       110.04        15.52       111.25         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
       51.22        68.61        81.93       106.75       110.53       121.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        19.76        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       19.92        13.32        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        34.82        34.26         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      316.73       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 
       41.23        32.61        34.03        24.16        35.84        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       57.11        38.76        42.54        22.32        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       45.83        53.69        12.99        24.82         1.61        23.77 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A822 TCGA-XG-A823 
       18.28        71.05        78.21        10.16       103.17        20.19 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               2.3                0.1 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             93.11             316.73 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            16.765             22.715 
[1] "2.3 - 93.1 (16.8)"  "0.1 - 316.7 (22.7)"
[1] "hr="     "2.5e+07"
D63V2, continuous
D63V3, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    2  4
  18Q LOSS WILD-TYPE 86 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2    4
  18Q LOSS WILD-TYPE   86   70
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                2                 86
  MALE                  4                 70
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0     1
  18Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                           1     4
  18Q LOSS WILD-TYPE                        18   130
D63V4, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       1                 18
  WHITE                                           4                130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = 19Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED     5   1
  19Q LOSS WILD-TYPE 151   5
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 6                156 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                  5 
$`19Q LOSS MUTATED`
TCGA-QR-A70R TCGA-SP-A6QG TCGA-SR-A6MQ TCGA-TT-A6YK TCGA-WB-A81S TCGA-WB-A820 
       14.20        67.50        68.61        25.15        23.77        10.16 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 
        9.93        14.27        31.53        15.58        32.15         1.28 
TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        4.11       116.19         0.23         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70W 
       29.92        13.12         9.01         1.41       117.14        41.79 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
        6.02        12.39        17.95        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        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       77.98         0.92       108.26        50.63         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        41.88         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89        20.09        31.59        30.21        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       31.04        26.96        40.70        37.58        30.51        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 
       20.58        25.32        12.66        18.94        18.08         9.73 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      114.77       109.25        82.62       110.04        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
        1.41         0.10        51.22        81.93       106.75       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      121.05         3.12        24.66        19.76        49.61         4.34 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       19.92        13.32        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        34.82        34.26         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      316.73       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 
       41.23        32.61        34.03        33.90        24.16        35.84 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        57.11        38.76        42.54        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       40.04        45.83        53.69        12.99        24.82         1.61 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       18.28        71.05        78.21        93.11       103.17        20.19 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             10.16               0.10 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             68.61             316.73 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            24.460             20.385 
[1] "10.2 - 68.6 (24.5)" "0.1 - 316.7 (20.4)"
[1] "hr=" "5.4"
D64V2, continuous
D64V3, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    3  3
  19Q LOSS WILD-TYPE 85 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3    3
  19Q LOSS WILD-TYPE   85   71
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                3                 85
  MALE                  3                 71
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     1
  19Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           0     5
  19Q LOSS WILD-TYPE                        19   129
D64V4, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  4
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           5                129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = 20Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     3   0
  20Q LOSS WILD-TYPE 153   6
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                159 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 0                  6 
$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 
       58.88        19.04         1.05        30.51         9.21        14.17 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A702 
        9.93        14.27        31.53        15.58        32.15         1.28 
TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        4.11       116.19         0.23         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70R 
       29.92        13.12         9.01         1.41       117.14        14.20 
TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK 
       41.79         6.02        12.39        17.95        36.23         6.94 
TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q 
        1.81         0.72        25.18         2.30         4.41         0.79 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       13.08        77.98       108.26        50.63         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        41.88         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89        20.09        31.59        30.21        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       31.04        26.96        40.70        37.58        30.51        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 
       20.58        25.32        12.66        18.94        18.08         9.73 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      114.77       109.25        82.62        67.50       110.04        15.52 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
      111.25         1.41         0.10        51.22        68.61        81.93 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
      106.75       110.53       121.05         3.12        24.66        19.76 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15        19.92        13.32        25.32 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HD TCGA-W2-A7HE 
       14.20        17.16         1.18        19.86        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       17.69        25.61        34.82        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       316.73       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        41.23        32.61        34.03        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       24.36        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
        1.61        23.77        18.28        71.05        78.21        10.16 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       93.11       103.17        20.19 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              0.92               0.10 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             12.03             316.73 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             10.65              23.11 
[1] "0.9 - 12.0 (10.7)"  "0.1 - 316.7 (23.1)"
[1] "hr="     "3300000"
D65V2, continuous
D65V3, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    2  1
  20Q LOSS WILD-TYPE 86 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    1
  20Q LOSS WILD-TYPE   86   73
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                2                 86
  MALE                  1                 73
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     0
  20Q LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           0     3
  20Q LOSS WILD-TYPE                        19   131
D65V4, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  5
  BLACK OR AFRICAN AMERICAN                       0                 19
  WHITE                                           3                131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = 21Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    36   0
  21Q LOSS WILD-TYPE 120   6
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                36                126 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 0                  6 
$`21Q LOSS MUTATED`
TCGA-PR-A5PF TCGA-QR-A6GO TCGA-QR-A6H2 TCGA-QR-A700 TCGA-QR-A70K TCGA-QR-A70N 
       17.95        35.01         9.93        32.15         9.01         1.41 
TCGA-QR-A70R TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RW-A67W 
       14.20         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        31.04        26.96       114.77       111.25 
TCGA-SR-A6MP TCGA-SR-A6MT TCGA-SR-A6MV TCGA-SR-A6MZ TCGA-TT-A6YK TCGA-TT-A6YN 
       51.22       106.75       121.05        19.76        25.15        19.92 
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        34.26         5.98 
TCGA-WB-A816 TCGA-WB-A819 TCGA-WB-A81H TCGA-WB-A81M TCGA-WB-A81S TCGA-WB-A821 
       41.23        33.90        42.54        45.83        23.77        93.11 

$`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        17.75         5.88        81.70 
TCGA-PR-A5PH TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GX 
       28.08        23.11         1.25       137.59        58.88        19.04 
TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H3 TCGA-QR-A6H5 
        1.05        30.51         9.21        14.17        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E 
       15.58         1.28         4.11       116.19         0.23         6.31 
TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70P TCGA-QR-A70W 
        2.33        26.83        29.92        13.12       117.14        41.79 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A5XN 
        6.02        12.39        17.95        36.23         1.81        25.18 
TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA 
        4.41        13.08        77.98         0.92       108.26        50.63 
TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 
        8.09        86.89         2.93         7.10        33.30        23.80 
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-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02        41.88         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WR 
       20.09        31.59        30.21        37.25        35.51        40.70 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       37.58        30.51        27.91        20.58        25.32        12.66 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       18.94        18.08         9.73       109.25        82.62        67.50 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MS 
      110.04        15.52         1.41         0.10        68.61        81.93 
TCGA-SR-A6MU TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YO 
      110.53         3.12        24.66        49.61         4.34        13.32 
TCGA-TT-A6YP TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       25.32        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        34.82         4.47         4.73         4.21       316.73 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A818 
      127.56        29.16        19.59        32.88        32.61        34.03 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81I 
       24.16        35.84        37.18        57.11        38.76        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       24.36        40.04        53.69        12.99        24.82         1.61 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A822 TCGA-XG-A823 
       18.28        71.05        78.21        10.16       103.17        20.19 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.72               0.10 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            121.05             316.73 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            19.890             22.715 
[1] "0.7 - 121.0 (19.9)" "0.1 - 316.7 (22.7)"
[1] "hr="     "2.6e+08"
D66V2, continuous
D66V3, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   21 15
  21Q LOSS WILD-TYPE 67 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     21   15
  21Q LOSS WILD-TYPE   67   59
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               21                 67
  MALE                 15                 59
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  1     2
  21Q LOSS WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                           3    30
  21Q LOSS WILD-TYPE                        16   104
D66V4, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                       3                 16
  WHITE                                          30                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(67) Variable = 22Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    53   5
  22Q LOSS WILD-TYPE 103   1
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                58                104 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 5                  1 
$`22Q LOSS MUTATED`
TCGA-P8-A5KD TCGA-P8-A6RY TCGA-PR-A5PF TCGA-QR-A6GR TCGA-QR-A6H6 TCGA-QR-A702 
        2.27         5.88        17.95        23.11        15.58         1.28 
TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70K TCGA-QR-A70P 
      116.19         6.31         2.33        26.83         9.01       117.14 
TCGA-QR-A70W TCGA-QT-A5XK TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-RT-A6Y9 
       41.79         6.94         2.30         4.41         0.79       108.26 
TCGA-RW-A67Y TCGA-RW-A681 TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WQ TCGA-S7-A7WR 
        7.10        23.80        31.59        30.21        26.96        40.70 
TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QJ TCGA-SP-A6QK 
       25.32        18.08        82.62        67.50        15.52       111.25 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MX TCGA-SR-A6MZ TCGA-TT-A6YK TCGA-W2-A7H5 
        0.10        51.22         3.12        19.76        25.15        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-A7UY TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 
       10.65         4.73         4.21        29.16        19.59         5.98 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81H TCGA-WB-A81N TCGA-WB-A81Q TCGA-WB-A81R 
       33.90        24.16        42.54        53.69        24.82         1.61 
TCGA-WB-A81T TCGA-WB-A81W TCGA-WB-A820 TCGA-XG-A823 
       18.28        78.21        10.16        20.19 

$`22Q LOSS WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A6RX TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO 
       31.46        29.03        17.75        81.70        28.08        35.01 
TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ 
        1.25       137.59        58.88        19.04         1.05        30.51 
TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A700 
        9.21        14.17         9.93        14.27        31.53        32.15 
TCGA-QR-A706 TCGA-QR-A70D TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70R 
        4.11         0.23        29.92        13.12         1.41        14.20 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A5XM 
        6.02        12.39        17.95        36.23         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6YA TCGA-RT-A6YC 
       25.18        13.08        77.98         0.92        50.63         8.09 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 
       86.89        19.86         2.93        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        41.88         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WT TCGA-S7-A7WU 
       20.09        37.25        35.51        31.04        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-SA-A6C2 TCGA-SP-A6QC 
       27.91        20.58        12.66        18.94         9.73       114.77 
TCGA-SP-A6QD TCGA-SP-A6QI TCGA-SQ-A6I4 TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT 
      109.25       110.04         1.41        68.61        81.93       106.75 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MY TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YN 
      110.53       121.05        24.66        49.61         4.34        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L 
       13.32        25.32        17.16        25.61        34.82        34.26 
TCGA-WB-A80M TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A817 
        4.47       316.73       127.56        32.88        41.23        32.61 
TCGA-WB-A818 TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81I 
       34.03        35.84        37.18        57.11        38.76        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81P TCGA-WB-A81S TCGA-WB-A81V 
       24.36        40.04        45.83        12.99        23.77        71.05 
TCGA-WB-A821 TCGA-WB-A822 
       93.11       103.17 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.10               0.23 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            117.14             316.73 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             18.18              25.25 
[1] "0.1 - 117.1 (18.2)" "0.2 - 316.7 (25.2)"
[1] "hr=" "12" 
D67V2, continuous
D67V3, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   33 25
  22Q LOSS WILD-TYPE 55 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     33   25
  22Q LOSS WILD-TYPE   55   49
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               33                 55
  MALE                 25                 49
[1] 2 2
[1] FALSE
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  1     2
  22Q LOSS WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                           6    49
  22Q LOSS WILD-TYPE                        13    85
D67V4, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                       6                 13
  WHITE                                          49                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = XP LOSS MUTATION ANALYSIS
D68V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    46   2
  XP LOSS WILD-TYPE 110   4
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               48               114 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                2                 4 
$`XP LOSS MUTATED`
TCGA-QR-A6GO TCGA-QR-A6GT TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A70H TCGA-QR-A70K 
       35.01       137.59        15.58         1.28        26.83         9.01 
TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK 
       14.20        41.79        12.39        17.95        36.23         6.94 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RT-A6YA TCGA-RW-A67Y TCGA-RW-A689 
       25.18         2.30         0.79        50.63         7.10        11.70 
TCGA-RW-A68A TCGA-RW-A68C TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WX TCGA-SP-A6QG 
       13.05         6.28        26.96        40.70        25.32        67.50 
TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-TT-A6YJ 
        0.10        68.61       121.05         3.12        24.66         4.34 
TCGA-TT-A6YN TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD 
       19.92        17.16         1.18        19.86        12.03        12.49 
TCGA-W2-A7HF TCGA-W2-A7UY TCGA-WB-A80M TCGA-WB-A80V TCGA-WB-A815 TCGA-WB-A819 
       17.69        10.65         4.47        29.16         5.98        33.90 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81K TCGA-WB-A81R TCGA-WB-A81W TCGA-WB-A820 
       37.18        57.11        40.04         1.61        78.21        10.16 

$`XP 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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GU TCGA-QR-A6GX 
       81.70        28.08        23.11         1.25        58.88        19.04 
TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
        1.05        30.51         9.21        14.17         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A700 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E 
       31.53        32.15         4.11       116.19         0.23         6.31 
TCGA-QR-A70G TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70X 
        2.33        29.92        13.12         1.41       117.14         6.02 
TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        1.81         0.72         4.41        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A680 
      108.26         8.09        86.89        19.86         2.93        33.30 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68B 
       23.80         1.05         0.85        13.32         1.22         7.96 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02        41.88         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        30.21        37.25        35.51        31.04 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X1 
       37.58        30.51        27.91        20.58        12.66        18.94 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QI 
       18.08         9.73       114.77       109.25        82.62       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MS TCGA-SR-A6MT 
       15.52       111.25         1.41        51.22        81.93       106.75 
TCGA-SR-A6MU TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YO TCGA-TT-A6YP 
      110.53        19.76        49.61        25.15        13.32        25.32 
TCGA-W2-A7H5 TCGA-W2-A7HE TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80N 
       14.20        16.60        25.61        34.82        34.26         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A816 
        4.21       316.73       127.56        19.59        32.88        41.23 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81G TCGA-WB-A81H 
       32.61        34.03        24.16        35.84        38.76        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       22.32        24.36        45.83        53.69        12.99        24.82 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       23.77        18.28        71.05        93.11       103.17        20.19 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.10              0.23 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           137.59            316.73 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           17.425            23.980 
[1] "0.1 - 137.6 (17.4)" "0.2 - 316.7 (24.0)"
[1] "hr=" "1.2"
D68V2, continuous
D68V3, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   25 23
  XP LOSS WILD-TYPE 63 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     25   23
  XP LOSS WILD-TYPE   63   51
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              25                63
  MALE                23                51
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP LOSS MUTATED                                  1     1
  XP LOSS WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED                           6    39
  XP LOSS WILD-TYPE                        13    95
D68V4, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      6                13
  WHITE                                         39                95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = XQ LOSS MUTATION ANALYSIS
D69V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    47   2
  XQ LOSS WILD-TYPE 109   4
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               49               113 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                 4 
$`XQ LOSS MUTATED`
TCGA-QR-A6GO TCGA-QR-A6GT TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A70H TCGA-QR-A70K 
       35.01       137.59        15.58         1.28        26.83         9.01 
TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK 
       14.20        41.79        12.39        17.95        36.23         6.94 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RT-A6YA TCGA-RW-A67Y TCGA-RW-A689 
       25.18         2.30         0.79        50.63         7.10        11.70 
TCGA-RW-A68A TCGA-RW-A68C TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WX TCGA-SP-A6QG 
       13.05         6.28        26.96        40.70        25.32        67.50 
TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-TT-A6YJ 
        0.10        68.61       121.05         3.12        24.66         4.34 
TCGA-TT-A6YN TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD 
       19.92        17.16         1.18        19.86        12.03        12.49 
TCGA-W2-A7HF TCGA-W2-A7UY TCGA-WB-A80M TCGA-WB-A80V TCGA-WB-A815 TCGA-WB-A819 
       17.69        10.65         4.47        29.16         5.98        33.90 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81K TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81W 
       37.18        57.11        40.04         1.61        23.77        78.21 
TCGA-WB-A820 
       10.16 

$`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        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GU TCGA-QR-A6GX 
       81.70        28.08        23.11         1.25        58.88        19.04 
TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 
        1.05        30.51         9.21        14.17         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A700 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E 
       31.53        32.15         4.11       116.19         0.23         6.31 
TCGA-QR-A70G TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70X 
        2.33        29.92        13.12         1.41       117.14         6.02 
TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        1.81         0.72         4.41        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A680 
      108.26         8.09        86.89        19.86         2.93        33.30 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68B 
       23.80         1.05         0.85        13.32         1.22         7.96 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02        41.88         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        30.21        37.25        35.51        31.04 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X1 
       37.58        30.51        27.91        20.58        12.66        18.94 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QI 
       18.08         9.73       114.77       109.25        82.62       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MS TCGA-SR-A6MT 
       15.52       111.25         1.41        51.22        81.93       106.75 
TCGA-SR-A6MU TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YO TCGA-TT-A6YP 
      110.53        19.76        49.61        25.15        13.32        25.32 
TCGA-W2-A7H5 TCGA-W2-A7HE TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80N 
       14.20        16.60        25.61        34.82        34.26         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A816 
        4.21       316.73       127.56        19.59        32.88        41.23 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81G TCGA-WB-A81H 
       32.61        34.03        24.16        35.84        38.76        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       22.32        24.36        45.83        53.69        12.99        24.82 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       18.28        71.05        93.11       103.17        20.19 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.10              0.23 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           137.59            316.73 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            17.69             24.16 
[1] "0.1 - 137.6 (17.7)" "0.2 - 316.7 (24.2)"
[1] "hr=" "1.2"
D69V2, continuous
D69V3, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   26 23
  XQ LOSS WILD-TYPE 62 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     26   23
  XQ LOSS WILD-TYPE   62   51
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              26                62
  MALE                23                51
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  1     1
  XQ LOSS WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           6    40
  XQ LOSS WILD-TYPE                        13    94
D69V4, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                 4
  BLACK OR AFRICAN AMERICAN                      6                13
  WHITE                                         40                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"
