[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/22506925/PCPG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PCPG-TP/22533878/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 70."
[1]  70 162
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6               156 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6               156 
[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 
               14               148 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               14               148 
[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 
               21               141 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               21               141 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                9               153 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                9               153 
[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 
                 6                156 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 6                156 
[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 
               97                65 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               97                65 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               25               137 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               25               137 
[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 
               60               102 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               60               102 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               87                75 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               87                75 
[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 
               18               144 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               18               144 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                7               155 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                7               155 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               21               141 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               21               141 
[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 
               12               150 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               12               150 
[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] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                159 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                159 
[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 
                62                100 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                62                100 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                15                147 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                15                147 
[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 
                 5                157 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 5                157 
[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] "TUMOR_TISSUE_SITE"                   
 [6] "GENDER"                              
 [7] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
 [8] "RADIATION_THERAPY"                   
 [9] "KARNOFSKY_PERFORMANCE_SCORE"         
[10] "HISTOLOGICAL_TYPE"                   
[11] "NUMBER_OF_LYMPH_NODES"               
[12] "RACE"                                
[13] "ETHNICITY"                           

Input Data has 13 rows and 162 columns.

[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=148,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 8:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 10:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'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"               
[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 8 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "TUMOR_TISSUE_SITE"          
[3] "GENDER"                      "RADIATION_THERAPY"          
[5] "KARNOFSKY_PERFORMANCE_SCORE" "HISTOLOGICAL_TYPE"          
[7] "NUMBER_OF_LYMPH_NODES"       "RACE"                       
YEARS_TO_BIRTH, nv=57, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=2, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=4, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=4, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED     6   0
  1P GAIN WILD-TYPE 150   6
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6               156 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                0                 6 
$`1P GAIN MUTATED`
TCGA-SR-A6MV TCGA-RW-A681 TCGA-S7-A7WL TCGA-SP-A6QC TCGA-SP-A6QD TCGA-WB-A81J 
      121.05        37.51        31.59       114.77       109.25        24.36 

$`1P GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 
       30.51        18.94         3.12        19.86        17.69        74.04 
TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY 
       43.07        48.53        24.82        10.16        20.19        31.46 
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       29.03         4.04        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-A6GX 
       28.08        35.01        23.11         1.25       137.59        19.04 
TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
        1.05         9.21         9.93        14.27        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.28         4.11       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W 
       29.92        13.12         9.01         1.41        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        47.64         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 
       19.30         1.22        27.22         6.28        72.79        11.57 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        2.89        20.09        36.56        37.25        35.51        31.04 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       40.70        42.77        27.91        23.21        25.32        17.95 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
       24.20         9.73        82.62        79.46       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-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      106.75       110.53        24.66        26.20        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       37.35        19.92        13.32        42.48        20.09        17.16 
TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY 
        1.18        14.43        18.44        16.60        25.61        14.79 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       41.26        34.26         4.47         4.73        25.51       316.73 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 
      127.56        29.16        19.59        53.59        41.23        42.35 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       33.90        24.16        35.84        57.11        38.76        63.98 
TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R 
       22.32        40.04        45.83        62.04        12.99         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       23.77        25.51        71.05        78.21        93.11       103.17 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            24.36              0.10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           121.05            316.73 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            73.38             24.43 
[1] "24.4 - 121.0 (73.4)" "0.1 - 316.7 (24.4)" 
[1] "hr="     "8.1e+07"
D1V2, continuous
D1V3, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     5   1
  1P GAIN WILD-TYPE 129  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      5    1
  1P GAIN WILD-TYPE  129   27
                    clus
vv                   1P GAIN MUTATED 1P GAIN WILD-TYPE
  ADRENAL GLAND                    5               129
  EXTRA-ADRENAL SITE               1                27
[1] 2 2
[1] FALSE
D1V4, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    1  5
  1P GAIN WILD-TYPE 87 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    5
  1P GAIN WILD-TYPE   87   69
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               1                87
  MALE                 5                69
[1] 2 2
[1] FALSE
D1V5, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     5   1
  1P GAIN WILD-TYPE 150   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      5    1
  1P GAIN WILD-TYPE  150    4
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                5               150
  YES               1                 4
[1] 2 2
[1] FALSE
D1V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  1P GAIN MUTATED               1                                             0
  1P GAIN WILD-TYPE            15                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  1P GAIN MUTATED                  5
  1P GAIN WILD-TYPE              130
D1V7, multiclass
                                               clus
vv                                              1P GAIN MUTATED
  PARAGANGLIOMA                                               1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                            5
                                               clus
vv                                              1P GAIN WILD-TYPE
  PARAGANGLIOMA                                                15
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, continuous
                   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     5
  1P GAIN WILD-TYPE                        19   129
D1V9, 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                                          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(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-QR-A70P TCGA-SR-A6MV TCGA-WB-A81Q TCGA-P7-A5NY TCGA-QR-A6GT TCGA-QR-A6GX 
      117.14       121.05        24.82        31.46       137.59        19.04 
TCGA-QR-A70R TCGA-RW-A680 TCGA-RW-A681 TCGA-S7-A7WL TCGA-SP-A6QC TCGA-SP-A6QD 
       14.20        47.64        37.51        31.59       114.77       109.25 
TCGA-SR-A6MZ TCGA-WB-A80P TCGA-WB-A815 TCGA-WB-A819 TCGA-WB-A81G TCGA-WB-A81J 
       26.20       316.73        53.59        33.90        38.76        24.36 
TCGA-WB-A81W 
       78.21 

$`1Q GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-RW-A68A 
       58.88        30.51        14.17        32.15         0.23        25.05 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU 
       23.90        44.52        41.88        13.87        26.96        30.51 
TCGA-S7-A7X1 TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 
       18.94         3.12        19.86        17.69        74.04        43.07 
TCGA-WB-A81E TCGA-WB-A820 TCGA-XG-A823 TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX 
       48.53        10.16        20.19        29.03         4.04        17.75 
TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR 
        5.88        17.95        81.70        28.08        35.01        23.11 
TCGA-QR-A6GS TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
        1.25         1.05         9.21         9.93        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G 
       15.58         1.28         4.11       116.19         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70W 
       26.83        29.92        13.12         9.01         1.41        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-A684 TCGA-RW-A685 TCGA-RW-A686 
       19.86         2.93         7.10         1.05         0.85        19.30 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
        1.22        27.22         6.28        72.79        11.57         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR 
       20.09        36.56        37.25        35.51        31.04        40.70 
TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 
       42.77        27.91        23.21        25.32        17.95        24.20 
TCGA-SA-A6C2 TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
        9.73        82.62        79.46       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-A6MY TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
      110.53        24.66        49.61         4.34        37.35        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC 
       13.32        42.48        20.09        17.16         1.18        14.43 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L 
       18.44        16.60        25.61        14.79        41.26        34.26 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.47         4.73        25.51       127.56        29.16        19.59 
TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81H 
       41.23        42.35        24.16        35.84        57.11        63.98 
TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R 
       22.32        40.04        45.83        62.04        12.99         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A821 TCGA-WB-A822 
       23.77        25.51        71.05        93.11       103.17 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             14.2               0.1 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           316.73            127.56 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            38.76             23.21 
[1] "14.2 - 316.7 (38.8)" "0.1 - 127.6 (23.2)" 
[1] "hr=" "1.6"
D2V2, continuous
D2V3, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    14   5
  1Q GAIN WILD-TYPE 120  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     14    5
  1Q GAIN WILD-TYPE  120   23
                    clus
vv                   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ADRENAL GLAND                   14               120
  EXTRA-ADRENAL SITE               5                23
[1] 2 2
[1] FALSE
D2V4, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    8 11
  1Q GAIN WILD-TYPE 80 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      8   11
  1Q GAIN WILD-TYPE   80   63
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               8                80
  MALE                11                63
[1] 2 2
[1] FALSE
D2V5, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    15   4
  1Q GAIN WILD-TYPE 140   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     15    4
  1Q GAIN WILD-TYPE  140    1
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               15               140
  YES               4                 1
[1] 2 2
[1] FALSE
D2V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  1Q GAIN MUTATED               2                                             2
  1Q GAIN WILD-TYPE            14                                             9
                   vv
clus                PHEOCHROMOCYTOMA
  1Q GAIN MUTATED                 15
  1Q GAIN WILD-TYPE              120
D2V7, multiclass
                                               clus
vv                                              1Q GAIN MUTATED
  PARAGANGLIOMA                                               2
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               2
  PHEOCHROMOCYTOMA                                           15
                                               clus
vv                                              1Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                14
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 9
  PHEOCHROMOCYTOMA                                            120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, continuous
                   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
D2V9, 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-RW-A68F TCGA-QR-A7IP TCGA-RW-A68D TCGA-WB-A81D 
       30.51        32.15        44.52        17.95        72.79        35.84 

$`2P GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A TCGA-RW-A68B 
       58.88        14.17         0.23       117.14        25.05        23.90 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV 
       41.88        13.87        26.96        30.51        18.94       121.05 
TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E 
        3.12        19.86        17.69        74.04        43.07        48.53 
TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD 
       24.82        10.16        20.19        31.46        29.03         4.04 
TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO 
       17.75         5.88        17.95        81.70        28.08        35.01 
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 
       23.11         1.25       137.59        19.04         1.05         9.21 
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-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
      116.19         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
        9.01         1.41        14.20        41.79         6.02        12.39 
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 
       47.64        37.51         1.05         0.85        19.30         1.22 
TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
       27.22         6.28        11.57         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT 
       36.56        37.25        35.51        31.04        40.70        42.77 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 
       27.91        23.21        25.32        17.95        24.20         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        79.46       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-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      106.75       110.53        24.66        26.20        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       37.35        19.92        13.32        42.48        20.09        17.16 
TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY 
        1.18        14.43        18.44        16.60        25.61        14.79 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       41.26        34.26         4.47         4.73        25.51       316.73 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 
      127.56        29.16        19.59        53.59        41.23        42.35 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       33.90        24.16        57.11        38.76        63.98        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R 
       24.36        40.04        45.83        62.04        12.99         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       23.77        25.51        71.05        78.21        93.11       103.17 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            17.95              0.10 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            72.79            316.73 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           33.995            24.510 
[1] "17.9 - 72.8 (34.0)" "0.1 - 316.7 (24.5)"
[1] "hr="     "2.6e+07"
D3V2, continuous
D3V3, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     5   1
  2P GAIN WILD-TYPE 129  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5    1
  2P GAIN WILD-TYPE  129   27
                    clus
vv                   2P GAIN MUTATED 2P GAIN WILD-TYPE
  ADRENAL GLAND                    5               129
  EXTRA-ADRENAL SITE               1                27
[1] 2 2
[1] FALSE
D3V4, 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
D3V5, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     6   0
  2P GAIN WILD-TYPE 149   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      6    0
  2P GAIN WILD-TYPE  149    5
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                6               149
  YES               0                 5
[1] 2 2
[1] FALSE
D3V6, continuous
[1] "Remove cluster labels:" "2P GAIN MUTATED"       
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                1                59 
       TCGA-S7-A7WQ        TCGA-S7-A7WU        TCGA-S7-A7X1        TCGA-SR-A6MV 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-WB-A817        TCGA-WB-A81E        TCGA-XG-A823        TCGA-P7-A5NY 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-PR-A5PF        TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-RT-A6YA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-RT-A6YC        TCGA-RX-A8JQ        TCGA-S7-A7WL        TCGA-S7-A7WM 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-S7-A7WN        TCGA-S7-A7WO        TCGA-S7-A7WP        TCGA-S7-A7WR 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-S7-A7WT        TCGA-S7-A7WV        TCGA-S7-A7WW        TCGA-S7-A7WX 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-S7-A7X0        TCGA-S7-A7X2        TCGA-SP-A6QC        TCGA-SP-A6QD 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-SP-A6QF        TCGA-SP-A6QG        TCGA-SP-A6QI        TCGA-SP-A6QJ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-SP-A6QK        TCGA-SR-A6MQ        TCGA-SR-A6MS        TCGA-SR-A6MY 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-SR-A6MZ        TCGA-SR-A6N0        TCGA-TT-A6YK        TCGA-TT-A6YN 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-TT-A6YO        TCGA-TT-A6YP        TCGA-WB-A80K        TCGA-WB-A80L 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-WB-A80Q        TCGA-WB-A815        TCGA-WB-A818        TCGA-WB-A81F 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-WB-A81G        TCGA-WB-A81H        TCGA-WB-A81I        TCGA-WB-A81J 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-WB-A81K        TCGA-WB-A81M        TCGA-WB-A81N        TCGA-WB-A81S 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-WB-A81T        TCGA-WB-A821        TCGA-WB-A822 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  2P GAIN MUTATED               1                                             0
  2P GAIN WILD-TYPE            15                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  2P GAIN MUTATED                  5
  2P GAIN WILD-TYPE              130
D3V7, multiclass
                                               clus
vv                                              2P GAIN MUTATED
  PARAGANGLIOMA                                               1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                            5
                                               clus
vv                                              2P GAIN WILD-TYPE
  PARAGANGLIOMA                                                15
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, continuous
                   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
D3V9, 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        41.26 

$`4P GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        14.17        32.15         0.23       117.14        25.05 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU 
       23.90        44.52        41.88        13.87        26.96        30.51 
TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 
       18.94       121.05         3.12        19.86        17.69        74.04 
TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY 
       43.07        48.53        24.82        10.16        20.19        31.46 
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       29.03         4.04        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-A6GX 
       28.08        35.01        23.11         1.25       137.59        19.04 
TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
        1.05         9.21         9.93        14.27        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.28         4.11       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W 
       29.92        13.12         9.01         1.41        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        47.64        37.51         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A7D0 
        0.85        19.30         1.22        27.22         6.28        11.57 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89        20.09        31.59        36.56        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       31.04        40.70        42.77        27.91        23.21        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       17.95        24.20         9.73       114.77       109.25        82.62 
TCGA-SP-A6QG TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
       79.46        15.52       111.25         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ 
       68.61        81.93       106.75       110.53        24.66        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        37.35        19.92        13.32        42.48 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       20.09        17.16         1.18        14.43        18.44        16.60 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       25.61        14.79        34.26         4.47         4.73        25.51 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 
      316.73       127.56        29.16        19.59        53.59        41.23 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G 
       42.35        33.90        24.16        35.84        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       63.98        22.32        24.36        40.04        45.83        62.04 
TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       12.99         1.61        23.77        25.51        71.05        78.21 
TCGA-WB-A821 TCGA-WB-A822 
       93.11       103.17 

  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 
           57.025            24.510 
[1] "30.5 - 110.0 (57.0)" "0.1 - 316.7 (24.5)" 
[1] "hr="     "2.6e+07"
D4V2, continuous
D4V3, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4   0
  4P GAIN WILD-TYPE 130  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    0
  4P GAIN WILD-TYPE  130   28
                    clus
vv                   4P GAIN MUTATED 4P GAIN WILD-TYPE
  ADRENAL GLAND                    4               130
  EXTRA-ADRENAL SITE               0                28
[1] 2 2
[1] FALSE
D4V4, 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
D4V5, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4   0
  4P GAIN WILD-TYPE 151   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    0
  4P GAIN WILD-TYPE  151    5
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                4               151
  YES               0                 5
[1] 2 2
[1] FALSE
D4V6, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                58 
       TCGA-S7-A7WQ        TCGA-S7-A7WU        TCGA-S7-A7X1        TCGA-SR-A6MV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-WB-A817        TCGA-WB-A81E        TCGA-XG-A823        TCGA-P7-A5NY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-PR-A5PF        TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-RT-A6YA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-RT-A6YC        TCGA-RX-A8JQ        TCGA-S7-A7WL        TCGA-S7-A7WM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-S7-A7WN        TCGA-S7-A7WO        TCGA-S7-A7WP        TCGA-S7-A7WR 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-S7-A7WT        TCGA-S7-A7WV        TCGA-S7-A7WW        TCGA-S7-A7WX 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-S7-A7X0        TCGA-S7-A7X2        TCGA-SP-A6QC        TCGA-SP-A6QD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-SP-A6QF        TCGA-SP-A6QG        TCGA-SP-A6QJ        TCGA-SP-A6QK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-SR-A6MQ        TCGA-SR-A6MS        TCGA-SR-A6MY        TCGA-SR-A6MZ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-SR-A6N0        TCGA-TT-A6YK        TCGA-TT-A6YN        TCGA-TT-A6YO 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-TT-A6YP        TCGA-WB-A80L        TCGA-WB-A80Q        TCGA-WB-A815 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-WB-A818        TCGA-WB-A81D        TCGA-WB-A81F        TCGA-WB-A81G 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-WB-A81H        TCGA-WB-A81I        TCGA-WB-A81J        TCGA-WB-A81K 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-WB-A81M        TCGA-WB-A81N        TCGA-WB-A81S        TCGA-WB-A81T 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-WB-A821        TCGA-WB-A822 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  4P GAIN MUTATED               0                                             0
  4P GAIN WILD-TYPE            16                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  4P GAIN MUTATED                  4
  4P GAIN WILD-TYPE              131
D4V7, multiclass
                                               clus
vv                                              4P GAIN MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                            4
                                               clus
vv                                              4P GAIN WILD-TYPE
  PARAGANGLIOMA                                                16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
                   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
D4V9, 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        41.26 

$`4Q GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 
       74.04        43.07        48.53        24.82        10.16        20.19 
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         4.04        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-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
       19.04         1.05         9.21         9.93        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G 
       15.58         1.28         4.11       116.19         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R 
       26.83        29.92        13.12         9.01         1.41        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        47.64        37.51 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D 
        1.05         0.85        19.30        27.22         6.28        72.79 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
       11.57         2.89        20.09        31.59        36.56        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW 
       35.51        31.04        40.70        42.77        27.91        23.21 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       25.32        17.95        24.20         9.73       114.77       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       82.62        79.46        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-A6MY 
       51.22        68.61        81.93       106.75       110.53        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       26.20        49.61         4.34        37.35        19.92        13.32 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD 
       42.48        20.09        17.16         1.18        14.43        18.44 
TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       16.60        25.61        14.79        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 
       25.51       316.73       127.56        29.16        19.59        53.59 
TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F 
       41.23        42.35        33.90        24.16        35.84        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        63.98        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       62.04        12.99         1.61        23.77        25.51        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       78.21        93.11       103.17 

  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 
            41.26             24.82 
[1] "1.2 - 110.0 (41.3)" "0.1 - 316.7 (24.8)"
[1] "hr="     "9200000"
D5V2, continuous
D5V3, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     3   0
  4Q GAIN WILD-TYPE 131  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3    0
  4Q GAIN WILD-TYPE  131   28
                    clus
vv                   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ADRENAL GLAND                    3               131
  EXTRA-ADRENAL SITE               0                28
[1] 2 2
[1] FALSE
D5V4, 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
D5V5, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     3   0
  4Q GAIN WILD-TYPE 152   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3    0
  4Q GAIN WILD-TYPE  152    5
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                3               152
  YES               0                 5
[1] 2 2
[1] FALSE
D5V6, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                58 
       TCGA-S7-A7WQ        TCGA-S7-A7WU        TCGA-S7-A7X1        TCGA-SR-A6MV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-WB-A817        TCGA-WB-A81E        TCGA-XG-A823        TCGA-P7-A5NY 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-PR-A5PF        TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-RT-A6YA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-RT-A6YC        TCGA-RX-A8JQ        TCGA-S7-A7WL        TCGA-S7-A7WM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S7-A7WN        TCGA-S7-A7WO        TCGA-S7-A7WP        TCGA-S7-A7WR 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S7-A7WT        TCGA-S7-A7WV        TCGA-S7-A7WW        TCGA-S7-A7WX 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-S7-A7X0        TCGA-S7-A7X2        TCGA-SP-A6QC        TCGA-SP-A6QD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-SP-A6QF        TCGA-SP-A6QG        TCGA-SP-A6QJ        TCGA-SP-A6QK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-SR-A6MQ        TCGA-SR-A6MS        TCGA-SR-A6MY        TCGA-SR-A6MZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-SR-A6N0        TCGA-TT-A6YK        TCGA-TT-A6YN        TCGA-TT-A6YO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-TT-A6YP        TCGA-WB-A80L        TCGA-WB-A80Q        TCGA-WB-A815 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-WB-A818        TCGA-WB-A81D        TCGA-WB-A81F        TCGA-WB-A81G 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-WB-A81H        TCGA-WB-A81I        TCGA-WB-A81J        TCGA-WB-A81K 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-WB-A81M        TCGA-WB-A81N        TCGA-WB-A81S        TCGA-WB-A81T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-WB-A821        TCGA-WB-A822 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  4Q GAIN MUTATED               0                                             0
  4Q GAIN WILD-TYPE            16                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  4Q GAIN MUTATED                  3
  4Q GAIN WILD-TYPE              132
D5V7, multiclass
                                               clus
vv                                              4Q GAIN MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                            3
                                               clus
vv                                              4Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            132
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, continuous
                   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
D5V9, 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        20.09 
TCGA-WB-A80K TCGA-WB-A815 TCGA-WB-A81A TCGA-WB-A81T TCGA-WB-A821 
       41.26        53.59        24.16        25.51        93.11 

$`5P GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 
       74.04        43.07        48.53        24.82        10.16        20.19 
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         4.04        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-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
        1.05         9.21         9.93        14.27        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.28         4.11       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
       29.92        13.12         1.41        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        47.64        37.51         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 
       19.30         1.22        27.22         6.28        72.79        11.57 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        2.89        20.09        36.56        37.25        35.51        31.04 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       40.70        42.77        27.91        23.21        25.32        17.95 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       24.20         9.73       114.77       109.25        82.62        79.46 
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-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ 
       68.61        81.93       110.53        24.66        26.20         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA 
       37.35        19.92        13.32        42.48        17.16         1.18 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80L 
       14.43        18.44        16.60        25.61        14.79        34.26 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73        25.51       316.73       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F 
       19.59        41.23        42.35        33.90        35.84        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        63.98        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81V TCGA-WB-A81W 
       62.04        12.99         1.61        23.77        71.05        78.21 
TCGA-WB-A822 
      103.17 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             9.01              0.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           106.75            316.73 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            31.59             24.66 
[1] "9.0 - 106.8 (31.6)" "0.1 - 316.7 (24.7)"
[1] "hr="     "7.5e+07"
D6V2, continuous
D6V3, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    11   0
  5P GAIN WILD-TYPE 123  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     11    0
  5P GAIN WILD-TYPE  123   28
                    clus
vv                   5P GAIN MUTATED 5P GAIN WILD-TYPE
  ADRENAL GLAND                   11               123
  EXTRA-ADRENAL SITE               0                28
[1] 2 2
[1] FALSE
D6V4, 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
D6V5, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    11   0
  5P GAIN WILD-TYPE 144   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     11    0
  5P GAIN WILD-TYPE  144    5
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               11               144
  YES               0                 5
[1] 2 2
[1] FALSE
D6V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  5P GAIN MUTATED               0                                             0
  5P GAIN WILD-TYPE            16                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  5P GAIN MUTATED                 11
  5P GAIN WILD-TYPE              124
D6V7, multiclass
                                               clus
vv                                              5P GAIN MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                           11
                                               clus
vv                                              5P GAIN WILD-TYPE
  PARAGANGLIOMA                                                16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, continuous
                   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
D6V9, 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        26.20        49.61        20.09        41.26 
TCGA-WB-A821 
       93.11 

$`5Q GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 
       74.04        43.07        48.53        24.82        10.16        20.19 
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         4.04        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-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
        1.05         9.21         9.93        14.27        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.28         4.11       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W 
       29.92        13.12         9.01         1.41        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        47.64        37.51         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D 
        0.85        19.30         1.22        27.22         6.28        72.79 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
       11.57         2.89        20.09        31.59        36.56        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW 
       35.51        31.04        40.70        42.77        27.91        23.21 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       25.32        17.95        24.20         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        79.46       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-A6MY 
        0.10        51.22        68.61        81.93       110.53        24.66 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 
        4.34        37.35        19.92        13.32        42.48        17.16 
TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY 
        1.18        14.43        18.44        16.60        25.61        14.79 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       34.26         4.47         4.73        25.51       316.73       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 
       29.16        19.59        53.59        41.23        42.35        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       24.16        35.84        57.11        38.76        63.98        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R 
       24.36        40.04        45.83        62.04        12.99         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 
       23.77        25.51        71.05        78.21       103.17 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            19.04              0.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           106.75            316.73 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            41.26             24.66 
[1] "19.0 - 106.8 (41.3)" "0.1 - 316.7 (24.7)" 
[1] "hr="     "2.6e+07"
D7V2, continuous
D7V3, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     7   0
  5Q GAIN WILD-TYPE 127  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7    0
  5Q GAIN WILD-TYPE  127   28
                    clus
vv                   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ADRENAL GLAND                    7               127
  EXTRA-ADRENAL SITE               0                28
[1] 2 2
[1] FALSE
D7V4, 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
D7V5, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     7   0
  5Q GAIN WILD-TYPE 148   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7    0
  5Q GAIN WILD-TYPE  148    5
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                7               148
  YES               0                 5
[1] 2 2
[1] FALSE
D7V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  5Q GAIN MUTATED               0                                             0
  5Q GAIN WILD-TYPE            16                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  5Q GAIN MUTATED                  7
  5Q GAIN WILD-TYPE              128
D7V7, multiclass
                                               clus
vv                                              5Q GAIN MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                            7
                                               clus
vv                                              5Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
                   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
D7V9, 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    14   0
  6P GAIN WILD-TYPE 142   6
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               14               148 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                0                 6 
$`6P GAIN MUTATED`
TCGA-QR-A6GZ TCGA-S7-A7X1 TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QR-A6GX 
       30.51        18.94         4.04        81.70        35.01        19.04 
TCGA-QR-A70N TCGA-RM-A68W TCGA-RW-A684 TCGA-S7-A7WN TCGA-W2-A7H5 TCGA-WB-A80L 
        1.41         0.92         1.05        37.25        20.09        34.26 
TCGA-WB-A819 TCGA-WB-A821 
       33.90        93.11 

$`6P GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        14.17        32.15         0.23       117.14        25.05 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU 
       23.90        44.52        41.88        13.87        26.96        30.51 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 
      121.05         3.12        19.86        17.69        74.04        43.07 
TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       48.53        24.82        10.16        20.19        31.46        29.03 
TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PH TCGA-QR-A6GR TCGA-QR-A6GS 
       17.75         5.88        17.95        28.08        23.11         1.25 
TCGA-QR-A6GT TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
      137.59         1.05         9.21         9.93        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G 
       15.58         1.28         4.11       116.19         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70W 
       26.83        29.92        13.12         9.01        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        47.64        37.51         0.85        19.30 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
        1.22        27.22         6.28        72.79        11.57         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR 
       20.09        31.59        36.56        35.51        31.04        40.70 
TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 
       42.77        27.91        23.21        25.32        17.95        24.20 
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        79.46       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-A6MT TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
       81.93       106.75       110.53        24.66        26.20        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 
        4.34        37.35        19.92        13.32        42.48        17.16 
TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY 
        1.18        14.43        18.44        16.60        25.61        14.79 
TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       41.26         4.47         4.73        25.51       316.73       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A81A 
       29.16        19.59        53.59        41.23        42.35        24.16 
TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       35.84        57.11        38.76        63.98        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        62.04        12.99         1.61        23.77 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 
       25.51        71.05        78.21       103.17 

  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 
           25.300            24.935 
[1] "0.9 - 93.1 (25.3)"  "0.1 - 316.7 (24.9)"
[1] "hr="     "7.5e+07"
D8V2, continuous
D8V3, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    13   1
  6P GAIN WILD-TYPE 121  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     13    1
  6P GAIN WILD-TYPE  121   27
                    clus
vv                   6P GAIN MUTATED 6P GAIN WILD-TYPE
  ADRENAL GLAND                   13               121
  EXTRA-ADRENAL SITE               1                27
[1] 2 2
[1] FALSE
D8V4, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    8  6
  6P GAIN WILD-TYPE 80 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      8    6
  6P GAIN WILD-TYPE   80   68
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               8                80
  MALE                 6                68
[1] 2 2
[1] FALSE
D8V5, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    14   0
  6P GAIN WILD-TYPE 141   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     14    0
  6P GAIN WILD-TYPE  141    5
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               14               141
  YES               0                 5
[1] 2 2
[1] FALSE
D8V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  6P GAIN MUTATED               0                                             1
  6P GAIN WILD-TYPE            16                                            10
                   vv
clus                PHEOCHROMOCYTOMA
  6P GAIN MUTATED                 13
  6P GAIN WILD-TYPE              122
D8V7, multiclass
                                               clus
vv                                              6P GAIN MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               1
  PHEOCHROMOCYTOMA                                           13
                                               clus
vv                                              6P GAIN WILD-TYPE
  PARAGANGLIOMA                                                16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                10
  PHEOCHROMOCYTOMA                                            122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, continuous
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                17 
       TCGA-QR-A70D        TCGA-QR-A70P        TCGA-WB-A814        TCGA-WB-A820 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-XG-A823        TCGA-PR-A5PH        TCGA-QR-A702        TCGA-QT-A5XJ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-QT-A5XP        TCGA-QT-A69Q        TCGA-RW-A680        TCGA-RW-A686 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-RW-A8AZ        TCGA-TT-A6YK        TCGA-WB-A80Q        TCGA-WB-A80Y 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-WB-A81W 
"6P GAIN WILD-TYPE" 
                   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    12
  6P GAIN WILD-TYPE                        17   122
D8V9, 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                                         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(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-A6GZ TCGA-S7-A7X1 TCGA-P8-A5KD TCGA-QR-A6GX TCGA-QR-A70N TCGA-W2-A7H5 
       30.51        18.94         4.04        19.04         1.41        20.09 
TCGA-WB-A80L TCGA-WB-A821 
       34.26        93.11 

$`6Q GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        14.17        32.15         0.23       117.14        25.05 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU 
       23.90        44.52        41.88        13.87        26.96        30.51 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 
      121.05         3.12        19.86        17.69        74.04        43.07 
TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       48.53        24.82        10.16        20.19        31.46        29.03 
TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO 
       17.75         5.88        17.95        81.70        28.08        35.01 
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 
       23.11         1.25       137.59         1.05         9.21         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-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-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        47.64 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 
       37.51         1.05         0.85        19.30         1.22        27.22 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        6.28        72.79        11.57         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT 
       36.56        37.25        35.51        31.04        40.70        42.77 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 
       27.91        23.21        25.32        17.95        24.20         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        79.46       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-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      106.75       110.53        24.66        26.20        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA 
       37.35        19.92        13.32        42.48        17.16         1.18 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       14.43        18.44        16.60        25.61        14.79        41.26 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73        25.51       316.73       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A 
       19.59        53.59        41.23        42.35        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       35.84        57.11        38.76        63.98        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        62.04        12.99         1.61        23.77 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 
       25.51        71.05        78.21       103.17 

  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 
           19.565            25.115 
[1] "1.4 - 93.1 (19.6)"  "0.1 - 316.7 (25.1)"
[1] "hr="     "2.6e+07"
D9V2, continuous
D9V3, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     8   0
  6Q GAIN WILD-TYPE 126  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      8    0
  6Q GAIN WILD-TYPE  126   28
                    clus
vv                   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ADRENAL GLAND                    8               126
  EXTRA-ADRENAL SITE               0                28
[1] 2 2
[1] FALSE
D9V4, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    5  3
  6Q GAIN WILD-TYPE 83 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      5    3
  6Q GAIN WILD-TYPE   83   71
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               5                83
  MALE                 3                71
[1] 2 2
[1] FALSE
D9V5, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     8   0
  6Q GAIN WILD-TYPE 147   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      8    0
  6Q GAIN WILD-TYPE  147    5
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                8               147
  YES               0                 5
[1] 2 2
[1] FALSE
D9V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  6Q GAIN MUTATED               0                                             0
  6Q GAIN WILD-TYPE            16                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  6Q GAIN MUTATED                  8
  6Q GAIN WILD-TYPE              127
D9V7, multiclass
                                               clus
vv                                              6Q GAIN MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                            8
                                               clus
vv                                              6Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, continuous
                   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
D9V9, 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-QR-A6GZ TCGA-QR-A700 TCGA-RW-A68G TCGA-S7-A7X1 TCGA-P8-A6RX TCGA-PR-A5PG 
       30.51        32.15        41.88        18.94        17.75        81.70 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A70N TCGA-QT-A5XM TCGA-QT-A69Q TCGA-QT-A7U0 
       19.04         1.05         1.41         0.72         0.79        13.08 
TCGA-RT-A6YC TCGA-RW-A681 TCGA-RW-A684 TCGA-S7-A7WL TCGA-S7-A7WW TCGA-SR-A6MT 
        8.09        37.51         1.05        31.59        23.21       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        25.51        53.59 
TCGA-WB-A81A TCGA-WB-A81N TCGA-WB-A821 
       24.16        62.04        93.11 

$`7P GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A TCGA-RW-A68B 
       58.88        14.17         0.23       117.14        25.05        23.90 
TCGA-RW-A68F TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-SR-A6MV TCGA-SR-A6MX 
       44.52        13.87        26.96        30.51       121.05         3.12 
TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q 
       19.86        17.69        74.04        43.07        48.53        24.82 
TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RY 
       10.16        20.19        31.46        29.03         4.04         5.88 
TCGA-PR-A5PF TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       17.95        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 
        9.21         9.93        14.27        31.53        15.58         1.28 
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-A70J TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
       13.12         9.01        14.20        41.79         6.02        12.39 
TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XN TCGA-QT-A5XO 
       17.95        36.23         6.94         1.81        25.18         2.30 
TCGA-QT-A5XP TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RW-A67V 
        4.41        77.98         0.92       108.26        50.63        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A685 TCGA-RW-A686 
       19.86         2.93         7.10        47.64         0.85        19.30 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
        1.22        27.22         6.28        72.79        11.57         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR 
       20.09        36.56        37.25        35.51        31.04        40.70 
TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 
       42.77        27.91        25.32        17.95        24.20         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        79.46       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-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       24.66        26.20         4.34        37.35        19.92        13.32 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       42.48        20.09         1.18        14.43        18.44        16.60 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80P 
       25.61        14.79        41.26         4.47         4.73       316.73 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 
      127.56        29.16        19.59        41.23        42.35        33.90 
TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       35.84        57.11        38.76        63.98        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        25.51 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 
       71.05        78.21       103.17 

  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 
            25.51             24.82 
[1] "0.7 - 110.5 (25.5)" "0.1 - 316.7 (24.8)"
[1] "hr="     "8.7e+07"
D10V2, continuous
D10V3, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    25   2
  7P GAIN WILD-TYPE 109  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     25    2
  7P GAIN WILD-TYPE  109   26
                    clus
vv                   7P GAIN MUTATED 7P GAIN WILD-TYPE
  ADRENAL GLAND                   25               109
  EXTRA-ADRENAL SITE               2                26
[1] 2 2
[1] FALSE
D10V4, 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
D10V5, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    27   0
  7P GAIN WILD-TYPE 128   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     27    0
  7P GAIN WILD-TYPE  128    5
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               27               128
  YES               0                 5
[1] 2 2
[1] FALSE
D10V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  7P GAIN MUTATED               1                                             1
  7P GAIN WILD-TYPE            15                                            10
                   vv
clus                PHEOCHROMOCYTOMA
  7P GAIN MUTATED                 25
  7P GAIN WILD-TYPE              110
D10V7, multiclass
                                               clus
vv                                              7P GAIN MUTATED
  PARAGANGLIOMA                                               1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               1
  PHEOCHROMOCYTOMA                                           25
                                               clus
vv                                              7P GAIN WILD-TYPE
  PARAGANGLIOMA                                                15
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                10
  PHEOCHROMOCYTOMA                                            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
[1] "Remove cluster labels:" "7P GAIN MUTATED"       
clus
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                2                16 
       TCGA-QR-A70D        TCGA-QR-A70P        TCGA-WB-A814        TCGA-WB-A820 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-XG-A823        TCGA-PR-A5PH        TCGA-QR-A702        TCGA-QT-A5XJ 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-QT-A5XP        TCGA-RW-A680        TCGA-RW-A686        TCGA-RW-A8AZ 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-TT-A6YK        TCGA-WB-A80Q        TCGA-WB-A80Y        TCGA-WB-A81W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
                   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
D10V9, 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    21   0
  7Q GAIN WILD-TYPE 135   6
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               21               141 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                0                 6 
$`7Q GAIN MUTATED`
TCGA-QR-A6GZ TCGA-QR-A700 TCGA-S7-A7X1 TCGA-P8-A6RX TCGA-QR-A6GX TCGA-QR-A70N 
       30.51        32.15        18.94        17.75        19.04         1.41 
TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RT-A6YC TCGA-RW-A681 TCGA-RW-A684 TCGA-RX-A8JQ 
        0.79        13.08         8.09        37.51         1.05        20.09 
TCGA-S7-A7WL TCGA-S7-A7WW TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6N0 TCGA-W2-A7H7 
       31.59        23.21       106.75       110.53        49.61        17.16 
TCGA-WB-A80L TCGA-WB-A81A TCGA-WB-A821 
       34.26        24.16        93.11 

$`7Q GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A TCGA-RW-A68B 
       58.88        14.17         0.23       117.14        25.05        23.90 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-SR-A6MV 
       44.52        41.88        13.87        26.96        30.51       121.05 
TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E 
        3.12        19.86        17.69        74.04        43.07        48.53 
TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD 
       24.82        10.16        20.19        31.46        29.03         4.04 
TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR 
        5.88        17.95        81.70        28.08        35.01        23.11 
TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 
        1.25       137.59         1.05         9.21         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E 
       31.53        15.58         1.28         4.11       116.19         6.31 
TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70R 
        2.33        26.83        29.92        13.12         9.01        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-RM-A68T 
        1.81         0.72        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        47.64         0.85        19.30         1.22        27.22 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-S7-A7WM TCGA-S7-A7WN 
        6.28        72.79        11.57         2.89        36.56        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WX 
       35.51        31.04        40.70        42.77        27.91        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       17.95        24.20         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 
       79.46       110.04        15.52       111.25         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ 
       51.22        68.61        81.93        24.66        26.20         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HA 
       37.35        19.92        13.32        42.48        20.09         1.18 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       14.43        18.44        16.60        25.61        14.79        41.26 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73        25.51       316.73       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D 
       19.59        53.59        41.23        42.35        33.90        35.84 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       57.11        38.76        63.98        22.32        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       45.83        62.04        12.99         1.61        23.77        25.51 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 
       71.05        78.21       103.17 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.79              0.10 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           110.53            316.73 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            23.21             25.18 
[1] "0.8 - 110.5 (23.2)" "0.1 - 316.7 (25.2)"
[1] "hr="     "8.1e+07"
D11V2, continuous
D11V3, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    18   3
  7Q GAIN WILD-TYPE 116  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     18    3
  7Q GAIN WILD-TYPE  116   25
                    clus
vv                   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ADRENAL GLAND                   18               116
  EXTRA-ADRENAL SITE               3                25
[1] 2 2
[1] FALSE
D11V4, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    8 13
  7Q GAIN WILD-TYPE 80 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      8   13
  7Q GAIN WILD-TYPE   80   61
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               8                80
  MALE                13                61
[1] 2 2
[1] FALSE
D11V5, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    21   0
  7Q GAIN WILD-TYPE 134   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     21    0
  7Q GAIN WILD-TYPE  134    5
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               21               134
  YES               0                 5
[1] 2 2
[1] FALSE
D11V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  7Q GAIN MUTATED               2                                             1
  7Q GAIN WILD-TYPE            14                                            10
                   vv
clus                PHEOCHROMOCYTOMA
  7Q GAIN MUTATED                 18
  7Q GAIN WILD-TYPE              117
D11V7, multiclass
                                               clus
vv                                              7Q GAIN MUTATED
  PARAGANGLIOMA                                               2
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               1
  PHEOCHROMOCYTOMA                                           18
                                               clus
vv                                              7Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                14
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                10
  PHEOCHROMOCYTOMA                                            117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, continuous
[1] "Remove cluster labels:" "7Q GAIN MUTATED"       
clus
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                1                17 
       TCGA-QR-A70D        TCGA-QR-A70P        TCGA-WB-A814        TCGA-WB-A820 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-XG-A823        TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-QR-A702 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-QT-A5XJ        TCGA-QT-A5XP        TCGA-RW-A680        TCGA-RW-A686 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-RW-A8AZ        TCGA-TT-A6YK        TCGA-WB-A80Q        TCGA-WB-A80Y 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-WB-A81W 
"7Q GAIN WILD-TYPE" 
                   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    19
  7Q GAIN WILD-TYPE                        17   115
D11V9, 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                                         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(12) Variable = 8P GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED     9   0
  8P GAIN WILD-TYPE 147   6
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                9               153 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                0                 6 
$`8P GAIN MUTATED`
TCGA-QR-A6GZ TCGA-QR-A70N TCGA-QR-A70R TCGA-RM-A68W TCGA-RW-A681 TCGA-S7-A7WW 
       30.51         1.41        14.20         0.92        37.51        23.21 
TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6N0 
       81.93       110.53        49.61 

$`8P GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        14.17        32.15         0.23       117.14        25.05 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU 
       23.90        44.52        41.88        13.87        26.96        30.51 
TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 
       18.94       121.05         3.12        19.86        17.69        74.04 
TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY 
       43.07        48.53        24.82        10.16        20.19        31.46 
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       29.03         4.04        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-A6GX 
       28.08        35.01        23.11         1.25       137.59        19.04 
TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
        1.05         9.21         9.93        14.27        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.28         4.11       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
       29.92        13.12         9.01        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 
       47.64         1.05         0.85        19.30         1.22        27.22 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        6.28        72.79        11.57         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT 
       36.56        37.25        35.51        31.04        40.70        42.77 
TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       27.91        25.32        17.95        24.20         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        79.46       110.04        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MT TCGA-SR-A6MY 
        1.41         0.10        51.22        68.61       106.75        24.66 
TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       26.20         4.34        37.35        19.92        13.32        42.48 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       20.09        17.16         1.18        14.43        18.44        16.60 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        14.79        41.26        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 
       25.51       316.73       127.56        29.16        19.59        53.59 
TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F 
       41.23        42.35        33.90        24.16        35.84        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        63.98        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       62.04        12.99         1.61        23.77        25.51        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       78.21        93.11       103.17 

  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 
            30.51             24.82 
[1] "0.9 - 110.5 (30.5)" "0.1 - 316.7 (24.8)"
[1] "hr="     "2.6e+07"
D12V2, continuous
D12V3, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     8   1
  8P GAIN WILD-TYPE 126  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      8    1
  8P GAIN WILD-TYPE  126   27
                    clus
vv                   8P GAIN MUTATED 8P GAIN WILD-TYPE
  ADRENAL GLAND                    8               126
  EXTRA-ADRENAL SITE               1                27
[1] 2 2
[1] FALSE
D12V4, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    4  5
  8P GAIN WILD-TYPE 84 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4    5
  8P GAIN WILD-TYPE   84   69
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               4                84
  MALE                 5                69
[1] 2 2
[1] FALSE
D12V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     9   0
  8P GAIN WILD-TYPE 146   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9    0
  8P GAIN WILD-TYPE  146    5
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                9               146
  YES               0                 5
[1] 2 2
[1] FALSE
D12V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  8P GAIN MUTATED               0                                             1
  8P GAIN WILD-TYPE            16                                            10
                   vv
clus                PHEOCHROMOCYTOMA
  8P GAIN MUTATED                  8
  8P GAIN WILD-TYPE              127
D12V7, multiclass
                                               clus
vv                                              8P GAIN MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               1
  PHEOCHROMOCYTOMA                                            8
                                               clus
vv                                              8P GAIN WILD-TYPE
  PARAGANGLIOMA                                                16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                10
  PHEOCHROMOCYTOMA                                            127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, continuous
                   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                           1     8
  8P GAIN WILD-TYPE                        18   126
D12V9, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P 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(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        37.51 
TCGA-RW-A8AZ TCGA-S7-A7WW TCGA-SP-A6QF TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6N0 
        2.89        23.21        82.62        81.93       110.53        49.61 
TCGA-W2-A7HE 
       16.60 

$`8Q GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        14.17        32.15         0.23       117.14        25.05 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU 
       23.90        44.52        41.88        13.87        26.96        30.51 
TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 
       18.94       121.05         3.12        19.86        17.69        74.04 
TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY 
       43.07        48.53        24.82        10.16        20.19        31.46 
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       29.03         4.04        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-A6GX 
       28.08        35.01        23.11         1.25       137.59        19.04 
TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
        1.05         9.21         9.93        14.27        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.28         4.11       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
       29.92        13.12         9.01        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        47.64 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C 
        1.05         0.85        19.30         1.22        27.22         6.28 
TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
       72.79        11.57        20.09        31.59        36.56        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WX 
       35.51        31.04        40.70        42.77        27.91        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG 
       17.95        24.20         9.73       114.77       109.25        79.46 
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-A6MT TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK 
       68.61       106.75        24.66        26.20         4.34        37.35 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       19.92        13.32        42.48        20.09        17.16         1.18 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L 
       14.43        18.44        25.61        14.79        41.26        34.26 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73        25.51       316.73       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A 
       19.59        53.59        41.23        42.35        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       35.84        57.11        38.76        63.98        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        62.04        12.99         1.61        23.77 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       25.51        71.05        78.21        93.11       103.17 

  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 
            25.18             24.82 
[1] "0.9 - 110.5 (25.2)" "0.1 - 316.7 (24.8)"
[1] "hr=" "2.9"
D13V2, continuous
D13V3, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    12   1
  8Q GAIN WILD-TYPE 122  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     12    1
  8Q GAIN WILD-TYPE  122   27
                    clus
vv                   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ADRENAL GLAND                   12               122
  EXTRA-ADRENAL SITE               1                27
[1] 2 2
[1] FALSE
D13V4, 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
D13V5, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    13   0
  8Q GAIN WILD-TYPE 142   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     13    0
  8Q GAIN WILD-TYPE  142    5
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               13               142
  YES               0                 5
[1] 2 2
[1] FALSE
D13V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  8Q GAIN MUTATED               0                                             1
  8Q GAIN WILD-TYPE            16                                            10
                   vv
clus                PHEOCHROMOCYTOMA
  8Q GAIN MUTATED                 12
  8Q GAIN WILD-TYPE              123
D13V7, multiclass
                                               clus
vv                                              8Q GAIN MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               1
  PHEOCHROMOCYTOMA                                           12
                                               clus
vv                                              8Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                10
  PHEOCHROMOCYTOMA                                            123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, continuous
[1] "Remove cluster labels:" "8Q GAIN MUTATED"       
clus
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                1                17 
       TCGA-QR-A70D        TCGA-QR-A70P        TCGA-WB-A814        TCGA-WB-A820 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-XG-A823        TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-QR-A702 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-QT-A5XJ        TCGA-QT-A5XP        TCGA-QT-A69Q        TCGA-RW-A680 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-RW-A686        TCGA-TT-A6YK        TCGA-WB-A80Q        TCGA-WB-A80Y 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-WB-A81W 
"8Q GAIN WILD-TYPE" 
                   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
D13V9, 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-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 
       74.04        43.07        48.53        24.82        10.16        20.19 
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         4.04        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-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
       19.04         1.05         9.21         9.93        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G 
       15.58         1.28         4.11       116.19         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70W 
       26.83        29.92        13.12         9.01        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        47.64        37.51         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D 
        0.85        19.30         1.22        27.22         6.28        72.79 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
       11.57         2.89        20.09        31.59        36.56        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW 
       35.51        31.04        40.70        42.77        27.91        23.21 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       25.32        17.95        24.20         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        79.46       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-A6MY 
        0.10        51.22        68.61        81.93       110.53        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       26.20        49.61         4.34        37.35        19.92        13.32 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       42.48        20.09         1.18        14.43        18.44        16.60 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       25.61        14.79        41.26         4.47         4.73        25.51 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 
      316.73       127.56        29.16        19.59        53.59        41.23 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G 
       42.35        33.90        24.16        35.84        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       63.98        22.32        24.36        40.04        45.83        62.04 
TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       12.99         1.61        23.77        25.51        71.05        78.21 
TCGA-WB-A821 TCGA-WB-A822 
       93.11       103.17 

  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 
           25.710            24.935 
[1] "1.4 - 106.8 (25.7)" "0.1 - 316.7 (24.9)"
[1] "hr="     "9200000"
D14V2, continuous
D14V3, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     4   0
  9P GAIN WILD-TYPE 130  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      4    0
  9P GAIN WILD-TYPE  130   28
                    clus
vv                   9P GAIN MUTATED 9P GAIN WILD-TYPE
  ADRENAL GLAND                    4               130
  EXTRA-ADRENAL SITE               0                28
[1] 2 2
[1] FALSE
D14V4, 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
D14V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     4   0
  9P GAIN WILD-TYPE 151   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      4    0
  9P GAIN WILD-TYPE  151    5
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                4               151
  YES               0                 5
[1] 2 2
[1] FALSE
D14V6, continuous
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                59 
       TCGA-S7-A7WQ        TCGA-S7-A7WU        TCGA-S7-A7X1        TCGA-SR-A6MV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-WB-A817        TCGA-WB-A81E        TCGA-XG-A823        TCGA-P7-A5NY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-PR-A5PF        TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-RT-A6YA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-RT-A6YC        TCGA-RX-A8JQ        TCGA-S7-A7WL        TCGA-S7-A7WM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-S7-A7WN        TCGA-S7-A7WO        TCGA-S7-A7WP        TCGA-S7-A7WR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-S7-A7WT        TCGA-S7-A7WV        TCGA-S7-A7WW        TCGA-S7-A7WX 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-S7-A7X0        TCGA-S7-A7X2        TCGA-SP-A6QC        TCGA-SP-A6QD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-SP-A6QF        TCGA-SP-A6QG        TCGA-SP-A6QI        TCGA-SP-A6QJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-SP-A6QK        TCGA-SR-A6MQ        TCGA-SR-A6MS        TCGA-SR-A6MY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-SR-A6MZ        TCGA-SR-A6N0        TCGA-TT-A6YK        TCGA-TT-A6YN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-TT-A6YO        TCGA-TT-A6YP        TCGA-WB-A80K        TCGA-WB-A80Q 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-WB-A815        TCGA-WB-A818        TCGA-WB-A81D        TCGA-WB-A81F 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-WB-A81G        TCGA-WB-A81H        TCGA-WB-A81I        TCGA-WB-A81J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-WB-A81K        TCGA-WB-A81M        TCGA-WB-A81N        TCGA-WB-A81S 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-WB-A81T        TCGA-WB-A821        TCGA-WB-A822 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  9P GAIN MUTATED               0                                             0
  9P GAIN WILD-TYPE            16                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  9P GAIN MUTATED                  4
  9P GAIN WILD-TYPE              131
D14V7, multiclass
                                               clus
vv                                              9P GAIN MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                            4
                                               clus
vv                                              9P GAIN WILD-TYPE
  PARAGANGLIOMA                                                16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, continuous
                   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
D14V9, 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-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 
       74.04        43.07        48.53        24.82        10.16        20.19 
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         4.04        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-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
       19.04         1.05         9.21         9.93        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G 
       15.58         1.28         4.11       116.19         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70W 
       26.83        29.92        13.12         9.01        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        47.64        37.51         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D 
        0.85        19.30         1.22        27.22         6.28        72.79 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
       11.57         2.89        20.09        31.59        36.56        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW 
       35.51        31.04        40.70        42.77        27.91        23.21 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       25.32        17.95        24.20         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        79.46       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-A6MY 
        0.10        51.22        68.61        81.93       110.53        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       26.20        49.61         4.34        37.35        19.92        13.32 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD 
       42.48        20.09        17.16         1.18        14.43        18.44 
TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N 
       16.60        25.61        14.79        41.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 
       25.51       316.73       127.56        29.16        19.59        53.59 
TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F 
       41.23        42.35        33.90        24.16        35.84        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        63.98        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       62.04        12.99         1.61        23.77        25.51        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       78.21        93.11       103.17 

  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             24.82 
[1] "1.4 - 106.8 (34.3)" "0.1 - 316.7 (24.8)"
[1] "hr="     "9200000"
D15V2, continuous
D15V3, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     3   0
  9Q GAIN WILD-TYPE 131  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    0
  9Q GAIN WILD-TYPE  131   28
                    clus
vv                   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ADRENAL GLAND                    3               131
  EXTRA-ADRENAL SITE               0                28
[1] 2 2
[1] FALSE
D15V4, 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
D15V5, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     3   0
  9Q GAIN WILD-TYPE 152   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    0
  9Q GAIN WILD-TYPE  152    5
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                3               152
  YES               0                 5
[1] 2 2
[1] FALSE
D15V6, continuous
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                59 
       TCGA-S7-A7WQ        TCGA-S7-A7WU        TCGA-S7-A7X1        TCGA-SR-A6MV 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-WB-A817        TCGA-WB-A81E        TCGA-XG-A823        TCGA-P7-A5NY 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-PR-A5PF        TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-RT-A6YA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-RT-A6YC        TCGA-RX-A8JQ        TCGA-S7-A7WL        TCGA-S7-A7WM 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-S7-A7WN        TCGA-S7-A7WO        TCGA-S7-A7WP        TCGA-S7-A7WR 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-S7-A7WT        TCGA-S7-A7WV        TCGA-S7-A7WW        TCGA-S7-A7WX 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-S7-A7X0        TCGA-S7-A7X2        TCGA-SP-A6QC        TCGA-SP-A6QD 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-SP-A6QF        TCGA-SP-A6QG        TCGA-SP-A6QI        TCGA-SP-A6QJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-SP-A6QK        TCGA-SR-A6MQ        TCGA-SR-A6MS        TCGA-SR-A6MY 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-SR-A6MZ        TCGA-SR-A6N0        TCGA-TT-A6YK        TCGA-TT-A6YN 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-TT-A6YO        TCGA-TT-A6YP        TCGA-WB-A80K        TCGA-WB-A80Q 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-WB-A815        TCGA-WB-A818        TCGA-WB-A81D        TCGA-WB-A81F 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-WB-A81G        TCGA-WB-A81H        TCGA-WB-A81I        TCGA-WB-A81J 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-WB-A81K        TCGA-WB-A81M        TCGA-WB-A81N        TCGA-WB-A81S 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-WB-A81T        TCGA-WB-A821        TCGA-WB-A822 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  9Q GAIN MUTATED               0                                             0
  9Q GAIN WILD-TYPE            16                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  9Q GAIN MUTATED                  3
  9Q GAIN WILD-TYPE              132
D15V7, multiclass
                                               clus
vv                                              9Q GAIN MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                            3
                                               clus
vv                                              9Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            132
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, continuous
                   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
D15V9, 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-A6H1 TCGA-RW-A68B TCGA-QR-A6GX TCGA-QR-A70N TCGA-RW-A681 TCGA-RW-A688 
       14.17        23.90        19.04         1.41        37.51         1.22 
TCGA-SR-A6MT TCGA-SR-A6MZ TCGA-W2-A7H5 TCGA-W2-A7HE TCGA-WB-A80L TCGA-WB-A81A 
      106.75        26.20        20.09        16.60        34.26        24.16 

$`10P GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        30.51        32.15         0.23       117.14        25.05 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7X1 
       44.52        41.88        13.87        26.96        30.51        18.94 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 
      121.05         3.12        19.86        17.69        74.04        43.07 
TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       48.53        24.82        10.16        20.19        31.46        29.03 
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH 
        4.04        17.75         5.88        17.95        81.70        28.08 
TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GY TCGA-QR-A6H0 
       35.01        23.11         1.25       137.59         1.05         9.21 
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-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
      116.19         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
        9.01        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-A689 TCGA-RW-A68C 
       47.64         1.05         0.85        19.30        27.22         6.28 
TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
       72.79        11.57         2.89        20.09        31.59        36.56 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV 
       37.25        35.51        31.04        40.70        42.77        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       23.21        25.32        17.95        24.20         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        79.46       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-A6MY TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       24.66        49.61         4.34        37.35        19.92        13.32 
TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HH 
       42.48        17.16         1.18        14.43        18.44        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       14.79        41.26         4.47         4.73        25.51       316.73 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 
      127.56        29.16        19.59        53.59        41.23        42.35 
TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       33.90        35.84        57.11        38.76        63.98        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R 
       24.36        40.04        45.83        62.04        12.99         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       23.77        25.51        71.05        78.21        93.11       103.17 

  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 
            21.995             25.250 
[1] "1.2 - 106.8 (22.0)" "0.1 - 316.7 (25.2)"
[1] "hr="     "2.7e+07"
D16V2, continuous
D16V3, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    12   0
  10P GAIN WILD-TYPE 122  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     12    0
  10P GAIN WILD-TYPE  122   28
                    clus
vv                   10P GAIN MUTATED 10P GAIN WILD-TYPE
  ADRENAL GLAND                    12                122
  EXTRA-ADRENAL SITE                0                 28
[1] 2 2
[1] FALSE
D16V4, 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
D16V5, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    12   0
  10P GAIN WILD-TYPE 143   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     12    0
  10P GAIN WILD-TYPE  143    5
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                12                143
  YES                0                  5
[1] 2 2
[1] FALSE
D16V6, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 58 
        TCGA-S7-A7WQ         TCGA-S7-A7WU         TCGA-S7-A7X1 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SR-A6MV         TCGA-WB-A817         TCGA-WB-A81E 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-XG-A823         TCGA-P7-A5NY         TCGA-PR-A5PF 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-PR-A5PG         TCGA-PR-A5PH         TCGA-RT-A6YA 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-RT-A6YC         TCGA-RX-A8JQ         TCGA-S7-A7WL 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-S7-A7WM         TCGA-S7-A7WN         TCGA-S7-A7WO 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-S7-A7WP         TCGA-S7-A7WR         TCGA-S7-A7WT 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-S7-A7WV         TCGA-S7-A7WW         TCGA-S7-A7WX 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-S7-A7X0         TCGA-S7-A7X2         TCGA-SP-A6QC 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SP-A6QD         TCGA-SP-A6QF         TCGA-SP-A6QG 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SP-A6QI         TCGA-SP-A6QJ         TCGA-SP-A6QK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SR-A6MQ         TCGA-SR-A6MS         TCGA-SR-A6MY 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SR-A6N0         TCGA-TT-A6YK         TCGA-TT-A6YN 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-TT-A6YO         TCGA-TT-A6YP         TCGA-WB-A80K 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-WB-A80Q         TCGA-WB-A815         TCGA-WB-A818 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-WB-A81D         TCGA-WB-A81F         TCGA-WB-A81G 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-WB-A81H         TCGA-WB-A81I         TCGA-WB-A81J 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-WB-A81K         TCGA-WB-A81M         TCGA-WB-A81N 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-WB-A81S         TCGA-WB-A81T         TCGA-WB-A821 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-WB-A822 
"10P GAIN WILD-TYPE" 
                    vv
clus                 PARAGANGLIOMA
  10P GAIN MUTATED               0
  10P GAIN WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  10P GAIN MUTATED                                               0
  10P GAIN WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  10P GAIN MUTATED                 12
  10P GAIN WILD-TYPE              123
D16V7, multiclass
                                               clus
vv                                              10P GAIN MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                            12
                                               clus
vv                                              10P GAIN WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, continuous
                    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
D16V9, 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-RW-A68B TCGA-QR-A70N TCGA-RW-A681 TCGA-RW-A688 TCGA-SP-A6QC 
       14.17        23.90         1.41        37.51         1.22       114.77 
TCGA-SR-A6MT TCGA-SR-A6MZ TCGA-W2-A7H5 TCGA-W2-A7HE 
      106.75        26.20        20.09        16.60 

$`10Q GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        30.51        32.15         0.23       117.14        25.05 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7X1 
       44.52        41.88        13.87        26.96        30.51        18.94 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 
      121.05         3.12        19.86        17.69        74.04        43.07 
TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       48.53        24.82        10.16        20.19        31.46        29.03 
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH 
        4.04        17.75         5.88        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-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 
        9.21         9.93        14.27        31.53        15.58         1.28 
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-A70J TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
       13.12         9.01        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        47.64         1.05         0.85        19.30        27.22 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        6.28        72.79        11.57         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT 
       36.56        37.25        35.51        31.04        40.70        42.77 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 
       27.91        23.21        25.32        17.95        24.20         9.73 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      109.25        82.62        79.46       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-A6MY TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       24.66        49.61         4.34        37.35        19.92        13.32 
TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HH 
       42.48        17.16         1.18        14.43        18.44        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       14.79        41.26        34.26         4.47         4.73        25.51 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 
      316.73       127.56        29.16        19.59        53.59        41.23 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G 
       42.35        33.90        24.16        35.84        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       63.98        22.32        24.36        40.04        45.83        62.04 
TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       12.99         1.61        23.77        25.51        71.05        78.21 
TCGA-WB-A821 TCGA-WB-A822 
       93.11       103.17 

  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 
            21.995             25.115 
[1] "1.2 - 114.8 (22.0)" "0.1 - 316.7 (25.1)"
[1] "hr="     "2.7e+07"
D17V2, continuous
D17V3, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    10   0
  10Q GAIN WILD-TYPE 124  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     10    0
  10Q GAIN WILD-TYPE  124   28
                    clus
vv                   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ADRENAL GLAND                    10                124
  EXTRA-ADRENAL SITE                0                 28
[1] 2 2
[1] FALSE
D17V4, 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
D17V5, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    10   0
  10Q GAIN WILD-TYPE 145   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     10    0
  10Q GAIN WILD-TYPE  145    5
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                10                145
  YES                0                  5
[1] 2 2
[1] FALSE
D17V6, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 58 
        TCGA-S7-A7WQ         TCGA-S7-A7WU         TCGA-S7-A7X1 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SR-A6MV         TCGA-WB-A817         TCGA-WB-A81E 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-XG-A823         TCGA-P7-A5NY         TCGA-PR-A5PF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-PR-A5PG         TCGA-PR-A5PH         TCGA-RT-A6YA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-RT-A6YC         TCGA-RX-A8JQ         TCGA-S7-A7WL 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-S7-A7WM         TCGA-S7-A7WN         TCGA-S7-A7WO 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-S7-A7WP         TCGA-S7-A7WR         TCGA-S7-A7WT 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-S7-A7WV         TCGA-S7-A7WW         TCGA-S7-A7WX 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-S7-A7X0         TCGA-S7-A7X2         TCGA-SP-A6QD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SP-A6QF         TCGA-SP-A6QG         TCGA-SP-A6QI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SP-A6QJ         TCGA-SP-A6QK         TCGA-SR-A6MQ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SR-A6MS         TCGA-SR-A6MY         TCGA-SR-A6N0 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-TT-A6YK         TCGA-TT-A6YN         TCGA-TT-A6YO 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-TT-A6YP         TCGA-WB-A80K         TCGA-WB-A80L 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WB-A80Q         TCGA-WB-A815         TCGA-WB-A818 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WB-A81D         TCGA-WB-A81F         TCGA-WB-A81G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WB-A81H         TCGA-WB-A81I         TCGA-WB-A81J 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WB-A81K         TCGA-WB-A81M         TCGA-WB-A81N 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WB-A81S         TCGA-WB-A81T         TCGA-WB-A821 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WB-A822 
"10Q GAIN WILD-TYPE" 
                    vv
clus                 PARAGANGLIOMA
  10Q GAIN MUTATED               0
  10Q GAIN WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  10Q GAIN MUTATED                                               0
  10Q GAIN WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  10Q GAIN MUTATED                 10
  10Q GAIN WILD-TYPE              125
D17V7, multiclass
                                               clus
vv                                              10Q GAIN MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                            10
                                               clus
vv                                              10Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, continuous
                    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
D17V9, 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 
        4.04        17.95        27.22        20.09        25.51 

$`11P GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 
       74.04        43.07        48.53        24.82        10.16        20.19 
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-A6GX TCGA-QR-A6GY 
       35.01        23.11         1.25       137.59        19.04         1.05 
TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 
        9.21         9.93        14.27        31.53        15.58         1.28 
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-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
       13.12         9.01         1.41        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        47.64        37.51         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
       19.30         1.22         6.28        72.79        11.57         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        36.56        37.25        35.51        31.04 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       40.70        42.77        27.91        23.21        25.32        17.95 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       24.20         9.73       114.77       109.25        82.62        79.46 
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-A6MY TCGA-SR-A6MZ 
       68.61        81.93       106.75       110.53        24.66        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        37.35        19.92        13.32        42.48 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       17.16         1.18        14.43        18.44        16.60        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80P 
       14.79        41.26        34.26         4.47         4.73       316.73 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 
      127.56        29.16        19.59        53.59        41.23        42.35 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       33.90        24.16        35.84        57.11        38.76        63.98 
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        62.04        12.99 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 
        1.61        23.77        25.51        71.05        78.21        93.11 
TCGA-WB-A822 
      103.17 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              4.04               0.10 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             27.22             316.73 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             20.09              25.05 
[1] "4.0 - 27.2 (20.1)"  "0.1 - 316.7 (25.1)"
[1] "hr="     "2.5e+07"
D18V2, continuous
D18V3, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     5   0
  11P GAIN WILD-TYPE 129  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5    0
  11P GAIN WILD-TYPE  129   28
                    clus
vv                   11P GAIN MUTATED 11P GAIN WILD-TYPE
  ADRENAL GLAND                     5                129
  EXTRA-ADRENAL SITE                0                 28
[1] 2 2
[1] FALSE
D18V4, 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
D18V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     5   0
  11P GAIN WILD-TYPE 150   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5    0
  11P GAIN WILD-TYPE  150    5
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 5                150
  YES                0                  5
[1] 2 2
[1] FALSE
D18V6, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 59 
        TCGA-S7-A7WQ         TCGA-S7-A7WU         TCGA-S7-A7X1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SR-A6MV         TCGA-WB-A817         TCGA-WB-A81E 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-XG-A823         TCGA-P7-A5NY         TCGA-PR-A5PG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-PR-A5PH         TCGA-RT-A6YA         TCGA-RT-A6YC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-RX-A8JQ         TCGA-S7-A7WL         TCGA-S7-A7WM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-S7-A7WN         TCGA-S7-A7WO         TCGA-S7-A7WP 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-S7-A7WR         TCGA-S7-A7WT         TCGA-S7-A7WV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-S7-A7WW         TCGA-S7-A7WX         TCGA-S7-A7X0 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-S7-A7X2         TCGA-SP-A6QC         TCGA-SP-A6QD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SP-A6QF         TCGA-SP-A6QG         TCGA-SP-A6QI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SP-A6QJ         TCGA-SP-A6QK         TCGA-SR-A6MQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SR-A6MS         TCGA-SR-A6MY         TCGA-SR-A6MZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-SR-A6N0         TCGA-TT-A6YK         TCGA-TT-A6YN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-TT-A6YO         TCGA-TT-A6YP         TCGA-WB-A80K 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-WB-A80L         TCGA-WB-A80Q         TCGA-WB-A815 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-WB-A818         TCGA-WB-A81D         TCGA-WB-A81F 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-WB-A81G         TCGA-WB-A81H         TCGA-WB-A81I 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-WB-A81J         TCGA-WB-A81K         TCGA-WB-A81M 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-WB-A81N         TCGA-WB-A81S         TCGA-WB-A81T 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-WB-A821         TCGA-WB-A822 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
                    vv
clus                 PARAGANGLIOMA
  11P GAIN MUTATED               0
  11P GAIN WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  11P GAIN MUTATED                                               0
  11P GAIN WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  11P GAIN MUTATED                  5
  11P GAIN WILD-TYPE              130
D18V7, multiclass
                                               clus
vv                                              11P GAIN MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                             5
                                               clus
vv                                              11P GAIN WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, continuous
                    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
D18V9, 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-A6GZ TCGA-QR-A700 TCGA-S7-A7X1 TCGA-QR-A6GX TCGA-QR-A70N TCGA-RW-A681 
       30.51        32.15        18.94        19.04         1.41        37.51 
TCGA-SR-A6MP TCGA-SR-A6MT TCGA-SR-A6MZ TCGA-W2-A7H5 TCGA-WB-A821 
       51.22       106.75        26.20        20.09        93.11 

$`12P GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A TCGA-RW-A68B 
       58.88        14.17         0.23       117.14        25.05        23.90 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-SR-A6MV 
       44.52        41.88        13.87        26.96        30.51       121.05 
TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E 
        3.12        19.86        17.69        74.04        43.07        48.53 
TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD 
       24.82        10.16        20.19        31.46        29.03         4.04 
TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO 
       17.75         5.88        17.95        81.70        28.08        35.01 
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 
       23.11         1.25       137.59         1.05         9.21         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-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-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        47.64 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C 
        1.05         0.85        19.30         1.22        27.22         6.28 
TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
       72.79        11.57         2.89        20.09        31.59        36.56 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV 
       37.25        35.51        31.04        40.70        42.77        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       23.21        25.32        17.95        24.20         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        79.46       110.04        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MY 
        1.41         0.10        68.61        81.93       110.53        24.66 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        37.35        19.92        13.32        42.48 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       17.16         1.18        14.43        18.44        16.60        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       14.79        41.26        34.26         4.47         4.73        25.51 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 
      316.73       127.56        29.16        19.59        53.59        41.23 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G 
       42.35        33.90        24.16        35.84        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       63.98        22.32        24.36        40.04        45.83        62.04 
TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       12.99         1.61        23.77        25.51        71.05        78.21 
TCGA-WB-A822 
      103.17 

  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 
             30.51              24.66 
[1] "1.4 - 106.8 (30.5)" "0.1 - 316.7 (24.7)"
[1] "hr="     "7.5e+07"
D19V2, continuous
D19V3, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    11   0
  12P GAIN WILD-TYPE 123  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     11    0
  12P GAIN WILD-TYPE  123   28
                    clus
vv                   12P GAIN MUTATED 12P GAIN WILD-TYPE
  ADRENAL GLAND                    11                123
  EXTRA-ADRENAL SITE                0                 28
[1] 2 2
[1] FALSE
D19V4, 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
D19V5, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    11   0
  12P GAIN WILD-TYPE 144   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     11    0
  12P GAIN WILD-TYPE  144    5
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                11                144
  YES                0                  5
[1] 2 2
[1] FALSE
D19V6, continuous
                    vv
clus                 PARAGANGLIOMA
  12P GAIN MUTATED               0
  12P GAIN WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  12P GAIN MUTATED                                               0
  12P GAIN WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  12P GAIN MUTATED                 11
  12P GAIN WILD-TYPE              124
D19V7, multiclass
                                               clus
vv                                              12P GAIN MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                            11
                                               clus
vv                                              12P GAIN WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, continuous
                    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
D19V9, 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-QR-A6GZ TCGA-QR-A700 TCGA-S7-A7X1 TCGA-PR-A5PF TCGA-QR-A6GX TCGA-QR-A70N 
       30.51        32.15        18.94        17.95        19.04         1.41 
TCGA-RW-A681 TCGA-S7-A7WN TCGA-SR-A6MP TCGA-SR-A6MT TCGA-SR-A6MZ TCGA-W2-A7H5 
       37.51        37.25        51.22       106.75        26.20        20.09 
TCGA-W2-A7HD TCGA-WB-A821 
       18.44        93.11 

$`12Q GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A TCGA-RW-A68B 
       58.88        14.17         0.23       117.14        25.05        23.90 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-SR-A6MV 
       44.52        41.88        13.87        26.96        30.51       121.05 
TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E 
        3.12        19.86        17.69        74.04        43.07        48.53 
TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD 
       24.82        10.16        20.19        31.46        29.03         4.04 
TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR 
       17.75         5.88        81.70        28.08        35.01        23.11 
TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 
        1.25       137.59         1.05         9.21         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E 
       31.53        15.58         1.28         4.11       116.19         6.31 
TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70R 
        2.33        26.83        29.92        13.12         9.01        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        47.64         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D 
        0.85        19.30         1.22        27.22         6.28        72.79 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WO 
       11.57         2.89        20.09        31.59        36.56        35.51 
TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       31.04        40.70        42.77        27.91        23.21        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       17.95        24.20         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 
       79.46       110.04        15.52       111.25         1.41         0.10 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6N0 TCGA-TT-A6YJ 
       68.61        81.93       110.53        24.66        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA 
       37.35        19.92        13.32        42.48        17.16         1.18 
TCGA-W2-A7HC TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L 
       14.43        16.60        25.61        14.79        41.26        34.26 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73        25.51       316.73       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A 
       19.59        53.59        41.23        42.35        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       35.84        57.11        38.76        63.98        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        62.04        12.99         1.61        23.77 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 
       25.51        71.05        78.21       103.17 

  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 
            28.355             24.740 
[1] "1.4 - 106.8 (28.4)" "0.1 - 316.7 (24.7)"
[1] "hr="     "7.7e+07"
D20V2, continuous
D20V3, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    14   0
  12Q GAIN WILD-TYPE 120  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     14    0
  12Q GAIN WILD-TYPE  120   28
                    clus
vv                   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ADRENAL GLAND                    14                120
  EXTRA-ADRENAL SITE                0                 28
[1] 2 2
[1] FALSE
D20V4, 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
D20V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    14   0
  12Q GAIN WILD-TYPE 141   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     14    0
  12Q GAIN WILD-TYPE  141    5
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                14                141
  YES                0                  5
[1] 2 2
[1] FALSE
D20V6, continuous
                    vv
clus                 PARAGANGLIOMA
  12Q GAIN MUTATED               0
  12Q GAIN WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  12Q GAIN MUTATED                                               0
  12Q GAIN WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  12Q GAIN MUTATED                 14
  12Q GAIN WILD-TYPE              121
D20V7, multiclass
                                               clus
vv                                              12Q GAIN MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                            14
                                               clus
vv                                              12Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, continuous
                    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
D20V9, 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-QR-A6GZ TCGA-RW-A68F TCGA-S7-A7X1 TCGA-P8-A6RX TCGA-QR-A70N TCGA-QT-A69Q 
       30.51        44.52        18.94        17.75         1.41         0.79 
TCGA-SR-A6MT TCGA-SR-A6N0 TCGA-WB-A821 
      106.75        49.61        93.11 

$`13Q GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        14.17        32.15         0.23       117.14        25.05 
TCGA-RW-A68B TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-SR-A6MV 
       23.90        41.88        13.87        26.96        30.51       121.05 
TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E 
        3.12        19.86        17.69        74.04        43.07        48.53 
TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD 
       24.82        10.16        20.19        31.46        29.03         4.04 
TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR 
        5.88        17.95        81.70        28.08        35.01        23.11 
TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 
        1.25       137.59        19.04         1.05         9.21         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-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-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-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        47.64        37.51 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C 
        1.05         0.85        19.30         1.22        27.22         6.28 
TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
       72.79        11.57         2.89        20.09        31.59        36.56 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV 
       37.25        35.51        31.04        40.70        42.77        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       23.21        25.32        17.95        24.20         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        79.46       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-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       24.66        26.20         4.34        37.35        19.92        13.32 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD 
       42.48        20.09        17.16         1.18        14.43        18.44 
TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       16.60        25.61        14.79        41.26        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73        25.51       316.73       127.56        29.16        19.59 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
       53.59        41.23        42.35        33.90        24.16        35.84 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       57.11        38.76        63.98        22.32        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       45.83        62.04        12.99         1.61        23.77        25.51 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 
       71.05        78.21       103.17 

  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 
             30.51              24.82 
[1] "0.8 - 106.8 (30.5)" "0.1 - 316.7 (24.8)"
[1] "hr="     "2.6e+07"
D21V2, continuous
D21V3, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     8   1
  13Q GAIN WILD-TYPE 126  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      8    1
  13Q GAIN WILD-TYPE  126   27
                    clus
vv                   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ADRENAL GLAND                     8                126
  EXTRA-ADRENAL SITE                1                 27
[1] 2 2
[1] FALSE
D21V4, 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
D21V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     9   0
  13Q GAIN WILD-TYPE 146   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      9    0
  13Q GAIN WILD-TYPE  146    5
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 9                146
  YES                0                  5
[1] 2 2
[1] FALSE
D21V6, continuous
                    vv
clus                 PARAGANGLIOMA
  13Q GAIN MUTATED               1
  13Q GAIN WILD-TYPE            15
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  13Q GAIN MUTATED                                               0
  13Q GAIN WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  13Q GAIN MUTATED                  8
  13Q GAIN WILD-TYPE              127
D21V7, multiclass
                                               clus
vv                                              13Q GAIN MUTATED
  PARAGANGLIOMA                                                1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                             8
                                               clus
vv                                              13Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                 15
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, continuous
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                 17 
        TCGA-QR-A70D         TCGA-QR-A70P         TCGA-WB-A814 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-WB-A820         TCGA-XG-A823         TCGA-PR-A5PG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-PR-A5PH         TCGA-QR-A702         TCGA-QT-A5XJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-QT-A5XP         TCGA-RW-A680         TCGA-RW-A686 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-RW-A8AZ         TCGA-TT-A6YK         TCGA-WB-A80Q 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-WB-A80Y         TCGA-WB-A81W 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
                    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
D21V9, 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-WB-A820 TCGA-QR-A70N TCGA-RW-A681 TCGA-SR-A6MT 
       10.16         1.41        37.51       106.75 

$`14Q GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-XG-A823 TCGA-P7-A5NY 
       74.04        43.07        48.53        24.82        20.19        31.46 
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       29.03         4.04        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-A6GX 
       28.08        35.01        23.11         1.25       137.59        19.04 
TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
        1.05         9.21         9.93        14.27        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.28         4.11       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
       29.92        13.12         9.01        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        47.64         1.05         0.85        19.30 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
        1.22        27.22         6.28        72.79        11.57         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        36.56        37.25        35.51        31.04 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       40.70        42.77        27.91        23.21        25.32        17.95 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       24.20         9.73       114.77       109.25        82.62        79.46 
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-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
       68.61        81.93       110.53        24.66        26.20        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        37.35        19.92        13.32        42.48        20.09 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       17.16         1.18        14.43        18.44        16.60        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       14.79        41.26        34.26         4.47         4.73        25.51 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 
      316.73       127.56        29.16        19.59        53.59        41.23 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G 
       42.35        33.90        24.16        35.84        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       63.98        22.32        24.36        40.04        45.83        62.04 
TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       12.99         1.61        23.77        25.51        71.05        78.21 
TCGA-WB-A821 TCGA-WB-A822 
       93.11       103.17 

  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 
            23.835             24.935 
[1] "1.4 - 106.8 (23.8)" "0.1 - 316.7 (24.9)"
[1] "hr=" "11" 
D22V2, continuous
D22V3, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     4   0
  14Q GAIN WILD-TYPE 130  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      4    0
  14Q GAIN WILD-TYPE  130   28
                    clus
vv                   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ADRENAL GLAND                     4                130
  EXTRA-ADRENAL SITE                0                 28
[1] 2 2
[1] FALSE
D22V4, 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
D22V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     4   0
  14Q GAIN WILD-TYPE 151   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      4    0
  14Q GAIN WILD-TYPE  151    5
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 4                151
  YES                0                  5
[1] 2 2
[1] FALSE
D22V6, continuous
                    vv
clus                 PARAGANGLIOMA
  14Q GAIN MUTATED               0
  14Q GAIN WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  14Q GAIN MUTATED                                               0
  14Q GAIN WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  14Q GAIN MUTATED                  4
  14Q GAIN WILD-TYPE              131
D22V7, multiclass
                                               clus
vv                                              14Q GAIN MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                             4
                                               clus
vv                                              14Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, continuous
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 17 
        TCGA-QR-A70D         TCGA-QR-A70P         TCGA-WB-A814 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-XG-A823         TCGA-PR-A5PG         TCGA-PR-A5PH 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QR-A702         TCGA-QT-A5XJ         TCGA-QT-A5XP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-QT-A69Q         TCGA-RW-A680         TCGA-RW-A686 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-RW-A8AZ         TCGA-TT-A6YK         TCGA-WB-A80Q 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-WB-A80Y         TCGA-WB-A81W 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
                    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
D22V9, 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-A700 TCGA-S7-A7X1 TCGA-QR-A6GX TCGA-QR-A70N TCGA-QR-A7IN TCGA-RW-A681 
       32.15        18.94        19.04         1.41        12.39        37.51 
TCGA-S7-A7WN TCGA-S7-A7WW TCGA-SP-A6QF TCGA-W2-A7H5 TCGA-W2-A7UY TCGA-WB-A80L 
       37.25        23.21        82.62        20.09        14.79        34.26 
TCGA-WB-A81A TCGA-WB-A81D 
       24.16        35.84 

$`15Q GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        30.51        14.17         0.23       117.14        25.05 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU 
       23.90        44.52        41.88        13.87        26.96        30.51 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 
      121.05         3.12        19.86        17.69        74.04        43.07 
TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       48.53        24.82        10.16        20.19        31.46        29.03 
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH 
        4.04        17.75         5.88        17.95        81.70        28.08 
TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GY TCGA-QR-A6H0 
       35.01        23.11         1.25       137.59         1.05         9.21 
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-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
      116.19         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IP TCGA-QT-A5XJ 
        9.01        14.20        41.79         6.02        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        47.64 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C 
        1.05         0.85        19.30         1.22        27.22         6.28 
TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
       72.79        11.57         2.89        20.09        31.59        36.56 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WX 
       35.51        31.04        40.70        42.77        27.91        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG 
       17.95        24.20         9.73       114.77       109.25        79.46 
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-A6MY TCGA-SR-A6MZ 
       68.61        81.93       106.75       110.53        24.66        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        37.35        19.92        13.32        42.48 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       17.16         1.18        14.43        18.44        16.60        25.61 
TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       41.26         4.47         4.73        25.51       316.73       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 
       29.16        19.59        53.59        41.23        42.35        33.90 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       57.11        38.76        63.98        22.32        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       45.83        62.04        12.99         1.61        23.77        25.51 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       71.05        78.21        93.11       103.17 

  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 
            23.685             25.115 
[1] "1.4 - 82.6 (23.7)"  "0.1 - 316.7 (25.1)"
[1] "hr="     "7.7e+07"
D23V2, continuous
D23V3, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    14   0
  15Q GAIN WILD-TYPE 120  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     14    0
  15Q GAIN WILD-TYPE  120   28
                    clus
vv                   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ADRENAL GLAND                    14                120
  EXTRA-ADRENAL SITE                0                 28
[1] 2 2
[1] FALSE
D23V4, 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
D23V5, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    14   0
  15Q GAIN WILD-TYPE 141   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     14    0
  15Q GAIN WILD-TYPE  141    5
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                14                141
  YES                0                  5
[1] 2 2
[1] FALSE
D23V6, continuous
                    vv
clus                 PARAGANGLIOMA
  15Q GAIN MUTATED               0
  15Q GAIN WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  15Q GAIN MUTATED                                               0
  15Q GAIN WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  15Q GAIN MUTATED                 14
  15Q GAIN WILD-TYPE              121
D23V7, multiclass
                                               clus
vv                                              15Q GAIN MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                            14
                                               clus
vv                                              15Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, continuous
                    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
D23V9, 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        37.51        20.09        51.22        20.09        24.16 

$`16P GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 
       74.04        43.07        48.53        24.82        10.16        20.19 
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         4.04        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-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
        1.05         9.21         9.93        14.27        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.28         4.11       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W 
       29.92        13.12         9.01         1.41        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        47.64         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 
       19.30         1.22        27.22         6.28        72.79        11.57 
TCGA-RW-A8AZ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        2.89        31.59        36.56        37.25        35.51        31.04 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       40.70        42.77        27.91        23.21        25.32        17.95 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       24.20         9.73       114.77       109.25        82.62        79.46 
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-SR-A6N0 
       81.93       106.75       110.53        24.66        26.20        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 
        4.34        37.35        19.92        13.32        42.48        17.16 
TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY 
        1.18        14.43        18.44        16.60        25.61        14.79 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       41.26        34.26         4.47         4.73        25.51       316.73 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 
      127.56        29.16        19.59        53.59        41.23        42.35 
TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       33.90        35.84        57.11        38.76        63.98        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R 
       24.36        40.04        45.83        62.04        12.99         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       23.77        25.51        71.05        78.21        93.11       103.17 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             19.04               0.10 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             51.22             316.73 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            22.125             25.115 
[1] "19.0 - 51.2 (22.1)" "0.1 - 316.7 (25.1)"
[1] "hr="     "2.6e+07"
D24V2, continuous
D24V3, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     5   1
  16P GAIN WILD-TYPE 129  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5    1
  16P GAIN WILD-TYPE  129   27
                    clus
vv                   16P GAIN MUTATED 16P GAIN WILD-TYPE
  ADRENAL GLAND                     5                129
  EXTRA-ADRENAL SITE                1                 27
[1] 2 2
[1] FALSE
D24V4, 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
D24V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     6   0
  16P GAIN WILD-TYPE 149   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      6    0
  16P GAIN WILD-TYPE  149    5
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 6                149
  YES                0                  5
[1] 2 2
[1] FALSE
D24V6, continuous
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 59 
        TCGA-S7-A7WQ         TCGA-S7-A7WU         TCGA-S7-A7X1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-SR-A6MV         TCGA-WB-A817         TCGA-WB-A81E 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-XG-A823         TCGA-P7-A5NY         TCGA-PR-A5PF 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-PR-A5PG         TCGA-PR-A5PH         TCGA-RT-A6YA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-RT-A6YC         TCGA-S7-A7WL         TCGA-S7-A7WM 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-S7-A7WN         TCGA-S7-A7WO         TCGA-S7-A7WP 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-S7-A7WR         TCGA-S7-A7WT         TCGA-S7-A7WV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-S7-A7WW         TCGA-S7-A7WX         TCGA-S7-A7X0 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-S7-A7X2         TCGA-SP-A6QC         TCGA-SP-A6QD 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-SP-A6QF         TCGA-SP-A6QG         TCGA-SP-A6QI 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-SP-A6QJ         TCGA-SP-A6QK         TCGA-SR-A6MQ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-SR-A6MS         TCGA-SR-A6MY         TCGA-SR-A6MZ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-SR-A6N0         TCGA-TT-A6YK         TCGA-TT-A6YN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-TT-A6YO         TCGA-TT-A6YP         TCGA-WB-A80K 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-WB-A80L         TCGA-WB-A80Q         TCGA-WB-A815 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-WB-A818         TCGA-WB-A81D         TCGA-WB-A81F 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-WB-A81G         TCGA-WB-A81H         TCGA-WB-A81I 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-WB-A81J         TCGA-WB-A81K         TCGA-WB-A81M 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-WB-A81N         TCGA-WB-A81S         TCGA-WB-A81T 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-WB-A821         TCGA-WB-A822 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
                    vv
clus                 PARAGANGLIOMA
  16P GAIN MUTATED               1
  16P GAIN WILD-TYPE            15
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  16P GAIN MUTATED                                               0
  16P GAIN WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  16P GAIN MUTATED                  5
  16P GAIN WILD-TYPE              130
D24V7, multiclass
                                               clus
vv                                              16P GAIN MUTATED
  PARAGANGLIOMA                                                1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                             5
                                               clus
vv                                              16P GAIN WILD-TYPE
  PARAGANGLIOMA                                                 15
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, continuous
                    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
D24V9, 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-WB-A820 TCGA-QR-A6GX TCGA-RW-A681 TCGA-RX-A8JQ TCGA-SR-A6MP TCGA-W2-A7H5 
       10.16        19.04        37.51        20.09        51.22        20.09 

$`16Q GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-XG-A823 TCGA-P7-A5NY 
       74.04        43.07        48.53        24.82        20.19        31.46 
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       29.03         4.04        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-A6GY 
       28.08        35.01        23.11         1.25       137.59         1.05 
TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 
        9.21         9.93        14.27        31.53        15.58         1.28 
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-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
       13.12         9.01         1.41        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        47.64         1.05         0.85        19.30 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
        1.22        27.22         6.28        72.79        11.57         2.89 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR 
       31.59        36.56        37.25        35.51        31.04        40.70 
TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 
       42.77        27.91        23.21        25.32        17.95        24.20 
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        79.46       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-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      106.75       110.53        24.66        26.20        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA 
       37.35        19.92        13.32        42.48        17.16         1.18 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       14.43        18.44        16.60        25.61        14.79        41.26 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       34.26         4.47         4.73        25.51       316.73       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 
       29.16        19.59        53.59        41.23        42.35        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       24.16        35.84        57.11        38.76        63.98        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R 
       24.36        40.04        45.83        62.04        12.99         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       23.77        25.51        71.05        78.21        93.11       103.17 

  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 
            20.090             25.115 
[1] "10.2 - 51.2 (20.1)" "0.1 - 316.7 (25.1)"
[1] "hr=" "6.1"
D25V2, continuous
D25V3, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     5   1
  16Q GAIN WILD-TYPE 129  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5    1
  16Q GAIN WILD-TYPE  129   27
                    clus
vv                   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ADRENAL GLAND                     5                129
  EXTRA-ADRENAL SITE                1                 27
[1] 2 2
[1] FALSE
D25V4, 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
D25V5, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     6   0
  16Q GAIN WILD-TYPE 149   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      6    0
  16Q GAIN WILD-TYPE  149    5
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 6                149
  YES                0                  5
[1] 2 2
[1] FALSE
D25V6, continuous
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 59 
        TCGA-S7-A7WQ         TCGA-S7-A7WU         TCGA-S7-A7X1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-SR-A6MV         TCGA-WB-A817         TCGA-WB-A81E 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-XG-A823         TCGA-P7-A5NY         TCGA-PR-A5PF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-PR-A5PG         TCGA-PR-A5PH         TCGA-RT-A6YA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-RT-A6YC         TCGA-S7-A7WL         TCGA-S7-A7WM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-S7-A7WN         TCGA-S7-A7WO         TCGA-S7-A7WP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-S7-A7WR         TCGA-S7-A7WT         TCGA-S7-A7WV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-S7-A7WW         TCGA-S7-A7WX         TCGA-S7-A7X0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-S7-A7X2         TCGA-SP-A6QC         TCGA-SP-A6QD 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-SP-A6QF         TCGA-SP-A6QG         TCGA-SP-A6QI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-SP-A6QJ         TCGA-SP-A6QK         TCGA-SR-A6MQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-SR-A6MS         TCGA-SR-A6MY         TCGA-SR-A6MZ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-SR-A6N0         TCGA-TT-A6YK         TCGA-TT-A6YN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-TT-A6YO         TCGA-TT-A6YP         TCGA-WB-A80K 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-WB-A80L         TCGA-WB-A80Q         TCGA-WB-A815 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-WB-A818         TCGA-WB-A81D         TCGA-WB-A81F 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-WB-A81G         TCGA-WB-A81H         TCGA-WB-A81I 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-WB-A81J         TCGA-WB-A81K         TCGA-WB-A81M 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-WB-A81N         TCGA-WB-A81S         TCGA-WB-A81T 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-WB-A821         TCGA-WB-A822 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
                    vv
clus                 PARAGANGLIOMA
  16Q GAIN MUTATED               1
  16Q GAIN WILD-TYPE            15
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  16Q GAIN MUTATED                                               0
  16Q GAIN WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  16Q GAIN MUTATED                  5
  16Q GAIN WILD-TYPE              130
D25V7, multiclass
                                               clus
vv                                              16Q GAIN MUTATED
  PARAGANGLIOMA                                                1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                             5
                                               clus
vv                                              16Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                 15
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, continuous
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 17 
        TCGA-QR-A70D         TCGA-QR-A70P         TCGA-WB-A814 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-XG-A823         TCGA-PR-A5PG         TCGA-PR-A5PH 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-QR-A702         TCGA-QT-A5XJ         TCGA-QT-A5XP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-QT-A69Q         TCGA-RW-A680         TCGA-RW-A686 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-RW-A8AZ         TCGA-TT-A6YK         TCGA-WB-A80Q 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-WB-A80Y         TCGA-WB-A81W 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
                    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
D25V9, 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   1
  17Q GAIN WILD-TYPE 151   5
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 6                156 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                  5 
$`17Q GAIN MUTATED`
TCGA-WB-A81Q TCGA-QR-A70K TCGA-RW-A681 TCGA-WB-A80P TCGA-WB-A81J TCGA-WB-A81W 
       24.82         9.01        37.51       316.73        24.36        78.21 

$`17Q GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY 
       74.04        43.07        48.53        10.16        20.19        31.46 
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       29.03         4.04        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-A6GX 
       28.08        35.01        23.11         1.25       137.59        19.04 
TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
        1.05         9.21         9.93        14.27        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.28         4.11       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
       29.92        13.12         1.41        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        47.64         1.05         0.85        19.30 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
        1.22        27.22         6.28        72.79        11.57         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        36.56        37.25        35.51        31.04 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       40.70        42.77        27.91        23.21        25.32        17.95 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       24.20         9.73       114.77       109.25        82.62        79.46 
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-A6MY TCGA-SR-A6MZ 
       68.61        81.93       106.75       110.53        24.66        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        37.35        19.92        13.32        42.48 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       20.09        17.16         1.18        14.43        18.44        16.60 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        14.79        41.26        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 
       25.51       127.56        29.16        19.59        53.59        41.23 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G 
       42.35        33.90        24.16        35.84        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       63.98        22.32        40.04        45.83        62.04        12.99 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A821 TCGA-WB-A822 
        1.61        23.77        25.51        71.05        93.11       103.17 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              9.01               0.10 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            316.73             137.59 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            31.165             24.855 
[1] "9.0 - 316.7 (31.2)" "0.1 - 137.6 (24.9)"
[1] "hr=" "2.8"
D26V2, continuous
D26V3, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     5   1
  17Q GAIN WILD-TYPE 129  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5    1
  17Q GAIN WILD-TYPE  129   27
                    clus
vv                   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ADRENAL GLAND                     5                129
  EXTRA-ADRENAL SITE                1                 27
[1] 2 2
[1] FALSE
D26V4, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    0  6
  17Q GAIN WILD-TYPE 88 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0    6
  17Q GAIN WILD-TYPE   88   68
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                0                 88
  MALE                  6                 68
[1] 2 2
[1] FALSE
D26V5, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     4   2
  17Q GAIN WILD-TYPE 151   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4    2
  17Q GAIN WILD-TYPE  151    3
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 4                151
  YES                2                  3
[1] 2 2
[1] FALSE
D26V6, continuous
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                 59 
        TCGA-S7-A7WQ         TCGA-S7-A7WU         TCGA-S7-A7X1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-SR-A6MV         TCGA-WB-A817         TCGA-WB-A81E 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-XG-A823         TCGA-P7-A5NY         TCGA-PR-A5PF 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-PR-A5PG         TCGA-PR-A5PH         TCGA-RT-A6YA 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-RT-A6YC         TCGA-RX-A8JQ         TCGA-S7-A7WL 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-S7-A7WM         TCGA-S7-A7WN         TCGA-S7-A7WO 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-S7-A7WP         TCGA-S7-A7WR         TCGA-S7-A7WT 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-S7-A7WV         TCGA-S7-A7WW         TCGA-S7-A7WX 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-S7-A7X0         TCGA-S7-A7X2         TCGA-SP-A6QC 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-SP-A6QD         TCGA-SP-A6QF         TCGA-SP-A6QG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-SP-A6QI         TCGA-SP-A6QJ         TCGA-SP-A6QK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-SR-A6MQ         TCGA-SR-A6MS         TCGA-SR-A6MY 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-SR-A6MZ         TCGA-SR-A6N0         TCGA-TT-A6YK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-TT-A6YN         TCGA-TT-A6YO         TCGA-TT-A6YP 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-WB-A80K         TCGA-WB-A80L         TCGA-WB-A80Q 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-WB-A815         TCGA-WB-A818         TCGA-WB-A81D 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-WB-A81F         TCGA-WB-A81G         TCGA-WB-A81H 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-WB-A81I         TCGA-WB-A81K         TCGA-WB-A81M 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-WB-A81N         TCGA-WB-A81S         TCGA-WB-A81T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-WB-A821         TCGA-WB-A822 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
                    vv
clus                 PARAGANGLIOMA
  17Q GAIN MUTATED               0
  17Q GAIN WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  17Q GAIN MUTATED                                               1
  17Q GAIN WILD-TYPE                                            10
                    vv
clus                 PHEOCHROMOCYTOMA
  17Q GAIN MUTATED                  5
  17Q GAIN WILD-TYPE              130
D26V7, multiclass
                                               clus
vv                                              17Q GAIN MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                1
  PHEOCHROMOCYTOMA                                             5
                                               clus
vv                                              17Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 10
  PHEOCHROMOCYTOMA                                             130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, continuous
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                 17 
        TCGA-QR-A70D         TCGA-QR-A70P         TCGA-WB-A814 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-WB-A820         TCGA-XG-A823         TCGA-PR-A5PG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-PR-A5PH         TCGA-QR-A702         TCGA-QT-A5XJ 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-QT-A5XP         TCGA-QT-A69Q         TCGA-RW-A680 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-RW-A686         TCGA-RW-A8AZ         TCGA-TT-A6YK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-WB-A80Q         TCGA-WB-A80Y 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
                    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                           0     6
  17Q GAIN WILD-TYPE                        19   128
D26V9, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q 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(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        37.51 
TCGA-SR-A6MT TCGA-WB-A80L 
      106.75        34.26 

$`18P GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A TCGA-RW-A68B 
       58.88        14.17         0.23       117.14        25.05        23.90 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7X1 
       44.52        41.88        13.87        26.96        30.51        18.94 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 
      121.05         3.12        19.86        17.69        74.04        43.07 
TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       48.53        24.82        10.16        20.19        31.46        29.03 
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH 
        4.04        17.75         5.88        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-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 
        9.21         9.93        14.27        31.53        15.58         1.28 
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-A70J TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
       13.12         9.01        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        47.64 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C 
        1.05         0.85        19.30         1.22        27.22         6.28 
TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
       72.79        11.57         2.89        20.09        31.59        36.56 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV 
       37.25        35.51        31.04        40.70        42.77        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       23.21        25.32        17.95        24.20         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        79.46       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-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        26.20        49.61         4.34        37.35        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC 
       13.32        42.48        20.09        17.16         1.18        14.43 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M 
       18.44        16.60        25.61        14.79        41.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73        25.51       316.73       127.56        29.16        19.59 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
       53.59        41.23        42.35        33.90        24.16        35.84 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       57.11        38.76        63.98        22.32        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       45.83        62.04        12.99         1.61        23.77        25.51 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       71.05        78.21        93.11       103.17 

  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 
            35.885             24.280 
[1] "1.4 - 106.8 (35.9)" "0.1 - 316.7 (24.3)"
[1] "hr="     "2.7e+07"
D27V2, continuous
D27V3, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     8   0
  18P GAIN WILD-TYPE 126  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      8    0
  18P GAIN WILD-TYPE  126   28
                    clus
vv                   18P GAIN MUTATED 18P GAIN WILD-TYPE
  ADRENAL GLAND                     8                126
  EXTRA-ADRENAL SITE                0                 28
[1] 2 2
[1] FALSE
D27V4, 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
D27V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     8   0
  18P GAIN WILD-TYPE 147   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      8    0
  18P GAIN WILD-TYPE  147    5
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 8                147
  YES                0                  5
[1] 2 2
[1] FALSE
D27V6, continuous
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 58 
        TCGA-S7-A7WQ         TCGA-S7-A7WU         TCGA-S7-A7X1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-SR-A6MV         TCGA-WB-A817         TCGA-WB-A81E 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-XG-A823         TCGA-P7-A5NY         TCGA-PR-A5PF 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-PR-A5PG         TCGA-PR-A5PH         TCGA-RT-A6YC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-RX-A8JQ         TCGA-S7-A7WL         TCGA-S7-A7WM 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-S7-A7WN         TCGA-S7-A7WO         TCGA-S7-A7WP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-S7-A7WR         TCGA-S7-A7WT         TCGA-S7-A7WV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-S7-A7WW         TCGA-S7-A7WX         TCGA-S7-A7X0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-S7-A7X2         TCGA-SP-A6QC         TCGA-SP-A6QD 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-SP-A6QF         TCGA-SP-A6QG         TCGA-SP-A6QI 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-SP-A6QJ         TCGA-SP-A6QK         TCGA-SR-A6MQ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-SR-A6MS         TCGA-SR-A6MY         TCGA-SR-A6MZ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-SR-A6N0         TCGA-TT-A6YK         TCGA-TT-A6YN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-TT-A6YO         TCGA-TT-A6YP         TCGA-WB-A80K 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-WB-A80Q         TCGA-WB-A815         TCGA-WB-A818 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-WB-A81D         TCGA-WB-A81F         TCGA-WB-A81G 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-WB-A81H         TCGA-WB-A81I         TCGA-WB-A81J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-WB-A81K         TCGA-WB-A81M         TCGA-WB-A81N 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-WB-A81S         TCGA-WB-A81T         TCGA-WB-A821 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-WB-A822 
"18P GAIN WILD-TYPE" 
                    vv
clus                 PARAGANGLIOMA
  18P GAIN MUTATED               0
  18P GAIN WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  18P GAIN MUTATED                                               0
  18P GAIN WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  18P GAIN MUTATED                  8
  18P GAIN WILD-TYPE              127
D27V7, multiclass
                                               clus
vv                                              18P GAIN MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                             8
                                               clus
vv                                              18P GAIN WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, continuous
                    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
D27V9, 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-QR-A6GZ TCGA-QR-A700 TCGA-P8-A5KD TCGA-QR-A70N TCGA-RT-A6YA TCGA-RW-A681 
       30.51        32.15         4.04         1.41        50.63        37.51 
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-QR-A6GU TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A TCGA-RW-A68B 
       58.88        14.17         0.23       117.14        25.05        23.90 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7X1 
       44.52        41.88        13.87        26.96        30.51        18.94 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 
      121.05         3.12        19.86        17.69        74.04        43.07 
TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       48.53        24.82        10.16        20.19        31.46        29.03 
TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO 
       17.75         5.88        17.95        81.70        28.08        35.01 
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 
       23.11         1.25       137.59        19.04         1.05         9.21 
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-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
      116.19         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
        9.01        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        47.64 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C 
        1.05         0.85        19.30         1.22        27.22         6.28 
TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
       72.79        11.57         2.89        20.09        31.59        36.56 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV 
       37.25        35.51        31.04        40.70        42.77        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       23.21        25.32        17.95        24.20         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        79.46       110.04        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MU TCGA-SR-A6MY 
        1.41         0.10        51.22        68.61       110.53        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       26.20        49.61         4.34        37.35        19.92        13.32 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD 
       42.48        20.09        17.16         1.18        14.43        18.44 
TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N 
       16.60        25.61        14.79        41.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 
       25.51       316.73       127.56        29.16        19.59        53.59 
TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F 
       41.23        42.35        33.90        24.16        35.84        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        63.98        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       62.04        12.99         1.61        23.77        25.51        71.05 
TCGA-WB-A821 TCGA-WB-A822 
       93.11       103.17 

  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 
            35.885             24.280 
[1] "1.4 - 106.8 (35.9)" "0.1 - 316.7 (24.3)"
[1] "hr="     "7.5e+07"
D28V2, continuous
D28V3, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    10   0
  18Q GAIN WILD-TYPE 124  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     10    0
  18Q GAIN WILD-TYPE  124   28
                    clus
vv                   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ADRENAL GLAND                    10                124
  EXTRA-ADRENAL SITE                0                 28
[1] 2 2
[1] FALSE
D28V4, 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
D28V5, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    10   0
  18Q GAIN WILD-TYPE 145   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     10    0
  18Q GAIN WILD-TYPE  145    5
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                10                145
  YES                0                  5
[1] 2 2
[1] FALSE
D28V6, continuous
                    vv
clus                 PARAGANGLIOMA
  18Q GAIN MUTATED               0
  18Q GAIN WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  18Q GAIN MUTATED                                               0
  18Q GAIN WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  18Q GAIN MUTATED                 10
  18Q GAIN WILD-TYPE              125
D28V7, multiclass
                                               clus
vv                                              18Q GAIN MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                            10
                                               clus
vv                                              18Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 17 
        TCGA-QR-A70D         TCGA-QR-A70P         TCGA-WB-A814 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-WB-A820         TCGA-XG-A823         TCGA-PR-A5PG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-PR-A5PH         TCGA-QR-A702         TCGA-QT-A5XJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-QT-A5XP         TCGA-QT-A69Q         TCGA-RW-A680 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-RW-A686         TCGA-RW-A8AZ         TCGA-TT-A6YK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-WB-A80Q         TCGA-WB-A80Y 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
                    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
D28V9, 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-A6GZ TCGA-WB-A81Q TCGA-QR-A6GX TCGA-QR-A6H6 TCGA-QR-A70N TCGA-RT-A6YA 
       30.51        24.82        19.04        15.58         1.41        50.63 
TCGA-RW-A681 TCGA-S7-A7WP TCGA-S7-A7WW TCGA-SQ-A6I6 TCGA-SR-A6MS TCGA-SR-A6MT 
       37.51        31.04        23.21         0.10        81.93       106.75 
TCGA-SR-A6N0 TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-WB-A80L TCGA-WB-A818 TCGA-WB-A81A 
       49.61        42.48        20.09        34.26        42.35        24.16 
TCGA-WB-A81H TCGA-WB-A81S 
       63.98        23.77 

$`19P GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        14.17        32.15         0.23       117.14        25.05 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU 
       23.90        44.52        41.88        13.87        26.96        30.51 
TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 
       18.94       121.05         3.12        19.86        17.69        74.04 
TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       43.07        48.53        10.16        20.19        31.46        29.03 
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH 
        4.04        17.75         5.88        17.95        81.70        28.08 
TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GY TCGA-QR-A6H0 
       35.01        23.11         1.25       137.59         1.05         9.21 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C 
        9.93        14.27        31.53         1.28         4.11       116.19 
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-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-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-A684 
       86.89        19.86         2.93         7.10        47.64         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D 
        0.85        19.30         1.22        27.22         6.28        72.79 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
       11.57         2.89        20.09        31.59        36.56        37.25 
TCGA-S7-A7WO TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X0 
       35.51        40.70        42.77        27.91        25.32        17.95 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       24.20         9.73       114.77       109.25        82.62        79.46 
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-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
      110.53        24.66        26.20         4.34        37.35        19.92 
TCGA-TT-A6YO TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       13.32        17.16         1.18        14.43        18.44        16.60 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       25.61        14.79        41.26         4.47         4.73        25.51 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 
      316.73       127.56        29.16        19.59        53.59        41.23 
TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81I TCGA-WB-A81J 
       33.90        35.84        57.11        38.76        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81T 
       40.04        45.83        62.04        12.99         1.61        25.51 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       71.05        78.21        93.11       103.17 

  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 
            30.775             24.510 
[1] "0.1 - 106.8 (30.8)" "0.2 - 316.7 (24.5)"
[1] "hr=" "1.5"
D29V2, continuous
D29V3, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    19   1
  19P GAIN WILD-TYPE 115  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     19    1
  19P GAIN WILD-TYPE  115   27
                    clus
vv                   19P GAIN MUTATED 19P GAIN WILD-TYPE
  ADRENAL GLAND                    19                115
  EXTRA-ADRENAL SITE                1                 27
[1] 2 2
[1] FALSE
D29V4, 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
D29V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    18   1
  19P GAIN WILD-TYPE 137   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     18    1
  19P GAIN WILD-TYPE  137    4
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                18                137
  YES                1                  4
[1] 2 2
[1] FALSE
D29V6, continuous
                    vv
clus                 PARAGANGLIOMA
  19P GAIN MUTATED               1
  19P GAIN WILD-TYPE            15
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  19P GAIN MUTATED                                               0
  19P GAIN WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  19P GAIN MUTATED                 19
  19P GAIN WILD-TYPE              116
D29V7, multiclass
                                               clus
vv                                              19P GAIN MUTATED
  PARAGANGLIOMA                                                1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                            19
                                               clus
vv                                              19P GAIN WILD-TYPE
  PARAGANGLIOMA                                                 15
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, continuous
                    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
D29V9, 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-A6GZ TCGA-QR-A6GX TCGA-QR-A70N TCGA-RW-A681 TCGA-S7-A7WW TCGA-SQ-A6I6 
       30.51        19.04         1.41        37.51        23.21         0.10 
TCGA-SR-A6MT TCGA-SR-A6N0 TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-WB-A80L TCGA-WB-A818 
      106.75        49.61        42.48        20.09        34.26        42.35 
TCGA-WB-A81A TCGA-WB-A81H 
       24.16        63.98 

$`19Q GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        14.17        32.15         0.23       117.14        25.05 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU 
       23.90        44.52        41.88        13.87        26.96        30.51 
TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 
       18.94       121.05         3.12        19.86        17.69        74.04 
TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY 
       43.07        48.53        24.82        10.16        20.19        31.46 
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       29.03         4.04        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-A6GY 
       28.08        35.01        23.11         1.25       137.59         1.05 
TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 
        9.21         9.93        14.27        31.53        15.58         1.28 
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-A70J TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
       13.12         9.01        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        47.64         1.05         0.85        19.30         1.22 
TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       27.22         6.28        72.79        11.57         2.89        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR 
       31.59        36.56        37.25        35.51        31.04        40.70 
TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 
       42.77        27.91        25.32        17.95        24.20         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        79.46       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-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       24.66        26.20         4.34        37.35        19.92        13.32 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       17.16         1.18        14.43        18.44        16.60        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       14.79        41.26         4.47         4.73        25.51       316.73 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A819 
      127.56        29.16        19.59        53.59        41.23        33.90 
TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       35.84        57.11        38.76        22.32        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       45.83        62.04        12.99         1.61        23.77        25.51 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       71.05        78.21        93.11       103.17 

  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 
            32.385             24.740 
[1] "0.1 - 106.8 (32.4)" "0.2 - 316.7 (24.7)"
[1] "hr="     "7.7e+07"
D30V2, continuous
D30V3, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    14   0
  19Q GAIN WILD-TYPE 120  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     14    0
  19Q GAIN WILD-TYPE  120   28
                    clus
vv                   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ADRENAL GLAND                    14                120
  EXTRA-ADRENAL SITE                0                 28
[1] 2 2
[1] FALSE
D30V4, 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
D30V5, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    13   0
  19Q GAIN WILD-TYPE 142   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     13    0
  19Q GAIN WILD-TYPE  142    5
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                13                142
  YES                0                  5
[1] 2 2
[1] FALSE
D30V6, continuous
                    vv
clus                 PARAGANGLIOMA
  19Q GAIN MUTATED               0
  19Q GAIN WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  19Q GAIN MUTATED                                               0
  19Q GAIN WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  19Q GAIN MUTATED                 14
  19Q GAIN WILD-TYPE              121
D30V7, multiclass
                                               clus
vv                                              19Q GAIN MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                            14
                                               clus
vv                                              19Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, continuous
                    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
D30V9, 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-QR-A6GZ TCGA-QR-A700 TCGA-PR-A5PF TCGA-RM-A68W TCGA-RW-A681 TCGA-SP-A6QI 
       30.51        32.15        17.95         0.92        37.51       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-QR-A6GU TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A TCGA-RW-A68B 
       58.88        14.17         0.23       117.14        25.05        23.90 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7X1 
       44.52        41.88        13.87        26.96        30.51        18.94 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 
      121.05         3.12        19.86        17.69        74.04        43.07 
TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       48.53        24.82        10.16        20.19        31.46        29.03 
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO 
        4.04        17.75         5.88        81.70        28.08        35.01 
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 
       23.11         1.25       137.59        19.04         1.05         9.21 
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-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
      116.19         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
        9.01         1.41        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 
       47.64         1.05         0.85        19.30         1.22        27.22 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        6.28        72.79        11.57         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT 
       36.56        37.25        35.51        31.04        40.70        42.77 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 
       27.91        23.21        25.32        17.95        24.20         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        79.46        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-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YO 
       24.66        26.20        49.61         4.34        37.35        13.32 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD 
       42.48        20.09        17.16         1.18        14.43        18.44 
TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80O 
       16.60        25.61        14.79        41.26         4.47        25.51 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 
      316.73       127.56        29.16        19.59        53.59        41.23 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       42.35        33.90        35.84        57.11        38.76        63.98 
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        62.04        12.99 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 
        1.61        23.77        25.51        71.05        78.21       103.17 

  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 
             31.33              24.74 
[1] "0.9 - 110.0 (31.3)" "0.1 - 316.7 (24.7)"
[1] "hr="     "7.5e+07"
D31V2, continuous
D31V3, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    11   1
  20P GAIN WILD-TYPE 123  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     11    1
  20P GAIN WILD-TYPE  123   27
                    clus
vv                   20P GAIN MUTATED 20P GAIN WILD-TYPE
  ADRENAL GLAND                    11                123
  EXTRA-ADRENAL SITE                1                 27
[1] 2 2
[1] FALSE
D31V4, 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
D31V5, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    12   0
  20P GAIN WILD-TYPE 143   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     12    0
  20P GAIN WILD-TYPE  143    5
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                12                143
  YES                0                  5
[1] 2 2
[1] FALSE
D31V6, continuous
                    vv
clus                 PARAGANGLIOMA
  20P GAIN MUTATED               0
  20P GAIN WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  20P GAIN MUTATED                                               1
  20P GAIN WILD-TYPE                                            10
                    vv
clus                 PHEOCHROMOCYTOMA
  20P GAIN MUTATED                 11
  20P GAIN WILD-TYPE              124
D31V7, multiclass
                                               clus
vv                                              20P GAIN MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                1
  PHEOCHROMOCYTOMA                                            11
                                               clus
vv                                              20P GAIN WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 10
  PHEOCHROMOCYTOMA                                             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, continuous
                    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
D31V9, 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-QR-A6GZ TCGA-QR-A700 TCGA-PR-A5PF TCGA-QR-A6GX TCGA-RW-A681 TCGA-SP-A6QI 
       30.51        32.15        17.95        19.04        37.51       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-QR-A6GU TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A TCGA-RW-A68B 
       58.88        14.17         0.23       117.14        25.05        23.90 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7X1 
       44.52        41.88        13.87        26.96        30.51        18.94 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 
      121.05         3.12        19.86        17.69        74.04        43.07 
TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       48.53        24.82        10.16        20.19        31.46        29.03 
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO 
        4.04        17.75         5.88        81.70        28.08        35.01 
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 
       23.11         1.25       137.59         1.05         9.21         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-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-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-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 
       47.64         1.05         0.85        19.30         1.22        27.22 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        6.28        72.79        11.57         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT 
       36.56        37.25        35.51        31.04        40.70        42.77 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 
       27.91        23.21        25.32        17.95        24.20         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        79.46        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-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        26.20        49.61         4.34        37.35        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC 
       13.32        42.48        20.09        17.16         1.18        14.43 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M 
       18.44        16.60        25.61        14.79        41.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73        25.51       316.73       127.56        29.16        19.59 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F 
       53.59        41.23        42.35        33.90        35.84        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        63.98        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       62.04        12.99         1.61        23.77        25.51        71.05 
TCGA-WB-A81W TCGA-WB-A822 
       78.21       103.17 

  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 
            33.205             24.510 
[1] "17.9 - 110.0 (33.2)" "0.1 - 316.7 (24.5)" 
[1] "hr="     "7.5e+07"
D32V2, continuous
D32V3, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    10   0
  20Q GAIN WILD-TYPE 124  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     10    0
  20Q GAIN WILD-TYPE  124   28
                    clus
vv                   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ADRENAL GLAND                    10                124
  EXTRA-ADRENAL SITE                0                 28
[1] 2 2
[1] FALSE
D32V4, 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
D32V5, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    10   0
  20Q GAIN WILD-TYPE 145   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     10    0
  20Q GAIN WILD-TYPE  145    5
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                10                145
  YES                0                  5
[1] 2 2
[1] FALSE
D32V6, continuous
                    vv
clus                 PARAGANGLIOMA
  20Q GAIN MUTATED               0
  20Q GAIN WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  20Q GAIN MUTATED                                               0
  20Q GAIN WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  20Q GAIN MUTATED                 10
  20Q GAIN WILD-TYPE              125
D32V7, multiclass
                                               clus
vv                                              20Q GAIN MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                            10
                                               clus
vv                                              20Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, continuous
                    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
D32V9, 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-A6GZ TCGA-S7-A7X1 TCGA-QR-A6GX 
       30.51        18.94        19.04 

$`21Q GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        14.17        32.15         0.23       117.14        25.05 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU 
       23.90        44.52        41.88        13.87        26.96        30.51 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 
      121.05         3.12        19.86        17.69        74.04        43.07 
TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       48.53        24.82        10.16        20.19        31.46        29.03 
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH 
        4.04        17.75         5.88        17.95        81.70        28.08 
TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GY TCGA-QR-A6H0 
       35.01        23.11         1.25       137.59         1.05         9.21 
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-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
      116.19         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
        9.01         1.41        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        47.64        37.51         1.05         0.85        19.30 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
        1.22        27.22         6.28        72.79        11.57         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        36.56        37.25        35.51        31.04 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       40.70        42.77        27.91        23.21        25.32        17.95 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       24.20         9.73       114.77       109.25        82.62        79.46 
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-A6MY TCGA-SR-A6MZ 
       68.61        81.93       106.75       110.53        24.66        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        37.35        19.92        13.32        42.48 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       20.09        17.16         1.18        14.43        18.44        16.60 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        14.79        41.26        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 
       25.51       316.73       127.56        29.16        19.59        53.59 
TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F 
       41.23        42.35        33.90        24.16        35.84        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        63.98        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       62.04        12.99         1.61        23.77        25.51        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       78.21        93.11       103.17 

  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              25.05 
[1] "18.9 - 30.5 (19.0)" "0.1 - 316.7 (25.1)"
[1] "hr="     "9200000"
D33V2, continuous
D33V3, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     3   0
  21Q GAIN WILD-TYPE 131  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    0
  21Q GAIN WILD-TYPE  131   28
                    clus
vv                   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ADRENAL GLAND                     3                131
  EXTRA-ADRENAL SITE                0                 28
[1] 2 2
[1] FALSE
D33V4, 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
D33V5, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     3   0
  21Q GAIN WILD-TYPE 152   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    0
  21Q GAIN WILD-TYPE  152    5
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 3                152
  YES                0                  5
[1] 2 2
[1] FALSE
D33V6, continuous
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                 59 
        TCGA-S7-A7WQ         TCGA-S7-A7WU         TCGA-SR-A6MV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-WB-A817         TCGA-WB-A81E         TCGA-XG-A823 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-P7-A5NY         TCGA-PR-A5PF         TCGA-PR-A5PG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-PR-A5PH         TCGA-RT-A6YA         TCGA-RT-A6YC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-RX-A8JQ         TCGA-S7-A7WL         TCGA-S7-A7WM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-S7-A7WN         TCGA-S7-A7WO         TCGA-S7-A7WP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-S7-A7WR         TCGA-S7-A7WT         TCGA-S7-A7WV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-S7-A7WW         TCGA-S7-A7WX         TCGA-S7-A7X0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-S7-A7X2         TCGA-SP-A6QC         TCGA-SP-A6QD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-SP-A6QF         TCGA-SP-A6QG         TCGA-SP-A6QI 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-SP-A6QJ         TCGA-SP-A6QK         TCGA-SR-A6MQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-SR-A6MS         TCGA-SR-A6MY         TCGA-SR-A6MZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-SR-A6N0         TCGA-TT-A6YK         TCGA-TT-A6YN 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-TT-A6YO         TCGA-TT-A6YP         TCGA-WB-A80K 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-WB-A80L         TCGA-WB-A80Q         TCGA-WB-A815 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-WB-A818         TCGA-WB-A81D         TCGA-WB-A81F 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-WB-A81G         TCGA-WB-A81H         TCGA-WB-A81I 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-WB-A81J         TCGA-WB-A81K         TCGA-WB-A81M 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-WB-A81N         TCGA-WB-A81S         TCGA-WB-A81T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-WB-A821         TCGA-WB-A822 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
                    vv
clus                 PARAGANGLIOMA
  21Q GAIN MUTATED               0
  21Q GAIN WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  21Q GAIN MUTATED                                               0
  21Q GAIN WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  21Q GAIN MUTATED                  3
  21Q GAIN WILD-TYPE              132
D33V7, multiclass
                                               clus
vv                                              21Q GAIN MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                             3
                                               clus
vv                                              21Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             132
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, continuous
                    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
D33V9, 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-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        30.51        14.17         0.23       117.14        25.05 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU 
       23.90        44.52        41.88        13.87        26.96        30.51 
TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 
       18.94       121.05         3.12        19.86        17.69        74.04 
TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY 
       43.07        48.53        24.82        10.16        20.19        31.46 
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       29.03         4.04        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-A6GX 
       28.08        35.01        23.11         1.25       137.59        19.04 
TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
        1.05         9.21         9.93        14.27        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.28         4.11       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
       29.92        13.12         9.01        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        47.64        37.51         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 
       19.30         1.22        27.22         6.28        72.79        11.57 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89        20.09        31.59        36.56        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       31.04        40.70        42.77        27.91        23.21        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       17.95        24.20         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 
       79.46       110.04        15.52       111.25         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ 
       51.22        68.61        81.93       110.53        24.66        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        37.35        19.92        13.32        42.48 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       20.09        17.16         1.18        14.43        18.44        16.60 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        14.79        41.26        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 
       25.51       316.73       127.56        29.16        19.59        53.59 
TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F 
       41.23        42.35        33.90        24.16        35.84        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        63.98        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       62.04        12.99         1.61        23.77        25.51        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       78.21        93.11       103.17 

  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              24.82 
[1] "1.4 - 106.8 (32.1)" "0.1 - 316.7 (24.8)"
[1] "hr="     "9200000"
D34V2, continuous
D34V3, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     3   0
  22Q GAIN WILD-TYPE 131  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3    0
  22Q GAIN WILD-TYPE  131   28
                    clus
vv                   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ADRENAL GLAND                     3                131
  EXTRA-ADRENAL SITE                0                 28
[1] 2 2
[1] FALSE
D34V4, 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
D34V5, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     3   0
  22Q GAIN WILD-TYPE 152   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3    0
  22Q GAIN WILD-TYPE  152    5
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 3                152
  YES                0                  5
[1] 2 2
[1] FALSE
D34V6, continuous
                    vv
clus                 PARAGANGLIOMA
  22Q GAIN MUTATED               0
  22Q GAIN WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  22Q GAIN MUTATED                                               0
  22Q GAIN WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  22Q GAIN MUTATED                  3
  22Q GAIN WILD-TYPE              132
D34V7, multiclass
                                               clus
vv                                              22Q GAIN MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                             3
                                               clus
vv                                              22Q GAIN WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             132
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, continuous
                    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
D34V9, 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        37.51       106.75        34.26        24.16 

$`XP GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 
       74.04        43.07        48.53        24.82        10.16        20.19 
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         4.04        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-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
        1.05         9.21         9.93        14.27        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
        1.28         4.11         6.31         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
       13.12         9.01         1.41        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        47.64         1.05         0.85        19.30 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
        1.22        27.22         6.28        72.79        11.57         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        36.56        37.25        35.51        31.04 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       40.70        42.77        27.91        23.21        25.32        17.95 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       24.20         9.73       114.77       109.25        82.62        79.46 
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-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
       68.61        81.93       110.53        24.66        26.20        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        37.35        19.92        13.32        42.48        20.09 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       17.16         1.18        14.43        18.44        16.60        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       14.79        41.26         4.47         4.73        25.51       316.73 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 
      127.56        29.16        19.59        53.59        41.23        42.35 
TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       33.90        35.84        57.11        38.76        63.98        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R 
       24.36        40.04        45.83        62.04        12.99         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       23.77        25.51        71.05        78.21        93.11       103.17 

  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 
           35.885            24.740 
[1] "19.0 - 116.2 (35.9)" "0.1 - 316.7 (24.7)" 
[1] "hr="     "2.6e+07"
D35V2, continuous
D35V3, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     6   0
  XP GAIN WILD-TYPE 128  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      6    0
  XP GAIN WILD-TYPE  128   28
                    clus
vv                   XP GAIN MUTATED XP GAIN WILD-TYPE
  ADRENAL GLAND                    6               128
  EXTRA-ADRENAL SITE               0                28
[1] 2 2
[1] FALSE
D35V4, 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
D35V5, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     6   0
  XP GAIN WILD-TYPE 149   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      6    0
  XP GAIN WILD-TYPE  149    5
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                6               149
  YES               0                 5
[1] 2 2
[1] FALSE
D35V6, continuous
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                1                59 
       TCGA-S7-A7WQ        TCGA-S7-A7WU        TCGA-S7-A7X1        TCGA-SR-A6MV 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-WB-A817        TCGA-WB-A81E        TCGA-XG-A823        TCGA-P7-A5NY 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-PR-A5PF        TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-RT-A6YA 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-RT-A6YC        TCGA-RX-A8JQ        TCGA-S7-A7WL        TCGA-S7-A7WM 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-S7-A7WN        TCGA-S7-A7WO        TCGA-S7-A7WP        TCGA-S7-A7WR 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-S7-A7WT        TCGA-S7-A7WV        TCGA-S7-A7WW        TCGA-S7-A7WX 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-S7-A7X0        TCGA-S7-A7X2        TCGA-SP-A6QC        TCGA-SP-A6QD 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-SP-A6QF        TCGA-SP-A6QG        TCGA-SP-A6QI        TCGA-SP-A6QJ 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-SP-A6QK        TCGA-SR-A6MQ        TCGA-SR-A6MS        TCGA-SR-A6MY 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-SR-A6MZ        TCGA-SR-A6N0        TCGA-TT-A6YK        TCGA-TT-A6YN 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-TT-A6YO        TCGA-TT-A6YP        TCGA-WB-A80K        TCGA-WB-A80Q 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-WB-A815        TCGA-WB-A818        TCGA-WB-A81D        TCGA-WB-A81F 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-WB-A81G        TCGA-WB-A81H        TCGA-WB-A81I        TCGA-WB-A81J 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-WB-A81K        TCGA-WB-A81M        TCGA-WB-A81N        TCGA-WB-A81S 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-WB-A81T        TCGA-WB-A821        TCGA-WB-A822 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  XP GAIN MUTATED               0                                             0
  XP GAIN WILD-TYPE            16                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  XP GAIN MUTATED                  6
  XP GAIN WILD-TYPE              129
D35V7, multiclass
                                               clus
vv                                              XP GAIN MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                            6
                                               clus
vv                                              XP GAIN WILD-TYPE
  PARAGANGLIOMA                                                16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, continuous
                   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
D35V9, 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        37.51       106.75        34.26        24.16 

$`XQ GAIN WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 
       74.04        43.07        48.53        24.82        10.16        20.19 
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         4.04        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-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
        1.05         9.21         9.93        14.27        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.28         4.11       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W 
       29.92        13.12         9.01         1.41        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        47.64         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 
       19.30         1.22        27.22         6.28        72.79        11.57 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89        20.09        31.59        36.56        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       31.04        40.70        42.77        27.91        23.21        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       17.95        24.20         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 
       79.46       110.04        15.52       111.25         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ 
       51.22        68.61        81.93       110.53        24.66        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        37.35        19.92        13.32        42.48 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       20.09        17.16         1.18        14.43        18.44        16.60 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       25.61        14.79        41.26         4.47         4.73        25.51 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 
      316.73       127.56        29.16        19.59        53.59        41.23 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       42.35        33.90        35.84        57.11        38.76        63.98 
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        62.04        12.99 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 
        1.61        23.77        25.51        71.05        78.21        93.11 
TCGA-WB-A822 
      103.17 

  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 
            34.26             24.82 
[1] "19.0 - 106.8 (34.3)" "0.1 - 316.7 (24.8)" 
[1] "hr="     "2.6e+07"
D36V2, continuous
D36V3, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     5   0
  XQ GAIN WILD-TYPE 129  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      5    0
  XQ GAIN WILD-TYPE  129   28
                    clus
vv                   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ADRENAL GLAND                    5               129
  EXTRA-ADRENAL SITE               0                28
[1] 2 2
[1] FALSE
D36V4, 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
D36V5, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     5   0
  XQ GAIN WILD-TYPE 150   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      5    0
  XQ GAIN WILD-TYPE  150    5
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                5               150
  YES               0                 5
[1] 2 2
[1] FALSE
D36V6, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                59 
       TCGA-S7-A7WQ        TCGA-S7-A7WU        TCGA-S7-A7X1        TCGA-SR-A6MV 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-WB-A817        TCGA-WB-A81E        TCGA-XG-A823        TCGA-P7-A5NY 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-PR-A5PF        TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-RT-A6YA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-RT-A6YC        TCGA-RX-A8JQ        TCGA-S7-A7WL        TCGA-S7-A7WM 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-S7-A7WN        TCGA-S7-A7WO        TCGA-S7-A7WP        TCGA-S7-A7WR 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-S7-A7WT        TCGA-S7-A7WV        TCGA-S7-A7WW        TCGA-S7-A7WX 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-S7-A7X0        TCGA-S7-A7X2        TCGA-SP-A6QC        TCGA-SP-A6QD 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-SP-A6QF        TCGA-SP-A6QG        TCGA-SP-A6QI        TCGA-SP-A6QJ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-SP-A6QK        TCGA-SR-A6MQ        TCGA-SR-A6MS        TCGA-SR-A6MY 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-SR-A6MZ        TCGA-SR-A6N0        TCGA-TT-A6YK        TCGA-TT-A6YN 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-TT-A6YO        TCGA-TT-A6YP        TCGA-WB-A80K        TCGA-WB-A80Q 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-WB-A815        TCGA-WB-A818        TCGA-WB-A81D        TCGA-WB-A81F 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-WB-A81G        TCGA-WB-A81H        TCGA-WB-A81I        TCGA-WB-A81J 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-WB-A81K        TCGA-WB-A81M        TCGA-WB-A81N        TCGA-WB-A81S 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-WB-A81T        TCGA-WB-A821        TCGA-WB-A822 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  XQ GAIN MUTATED               0                                             0
  XQ GAIN WILD-TYPE            16                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  XQ GAIN MUTATED                  5
  XQ GAIN WILD-TYPE              130
D36V7, multiclass
                                               clus
vv                                              XQ GAIN MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                            5
                                               clus
vv                                              XQ GAIN WILD-TYPE
  PARAGANGLIOMA                                                16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, continuous
                   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
D36V9, 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   95  2
  1P LOSS WILD-TYPE 61  4
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               97                65 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                 4 
$`1P LOSS MUTATED`
TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A TCGA-RW-A68B 
       14.17        32.15         0.23       117.14        25.05        23.90 
TCGA-S7-A7WQ TCGA-S7-A7X1 TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A81E TCGA-WB-A81Q 
       26.96        18.94        19.86        17.69        48.53        24.82 
TCGA-P7-A5NY TCGA-P8-A5KD TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO 
       31.46         4.04        17.95        81.70        28.08        35.01 
TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H6 
      137.59        19.04         9.21         9.93        14.27        15.58 
TCGA-QR-A70E TCGA-QR-A70H TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70W 
        6.31        26.83        13.12         9.01        14.20        41.79 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XO 
        6.02        12.39        17.95         6.94         0.72         2.30 
TCGA-QT-A69Q TCGA-RM-A68T TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.79        77.98        50.63         8.09        86.89        19.86 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
        7.10        47.64         1.05         0.85        19.30         1.22 
TCGA-RW-A689 TCGA-RW-A7D0 TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WR TCGA-S7-A7WX 
       27.22        11.57        20.09        37.25        40.70        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
       17.95        24.20        82.62        79.46       110.04        15.52 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT 
      111.25         1.41         0.10        68.61        81.93       106.75 
TCGA-SR-A6MU TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-W2-A7H5 
      110.53        26.20         4.34        37.35        19.92        20.09 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7UY 
       17.16         1.18        14.43        18.44        16.60        14.79 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A816 
        4.47         4.73        25.51       316.73        29.16        41.23 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81K 
       42.35        33.90        35.84        38.76        63.98        40.04 
TCGA-WB-A81M TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 
       45.83         1.61        25.51        71.05        78.21        93.11 
TCGA-WB-A822 
      103.17 

$`1P LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WU 
       58.88        30.51        44.52        41.88        13.87        30.51 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A820 TCGA-XG-A823 
      121.05         3.12        74.04        43.07        10.16        20.19 
TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GY 
       29.03        17.75         5.88        23.11         1.25         1.05 
TCGA-QR-A6H5 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70G TCGA-QR-A70I 
       31.53         1.28         4.11       116.19         2.33        29.92 
TCGA-QR-A70N TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A7U0 
        1.41        36.23         1.81        25.18         4.41        13.08 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RW-A67X TCGA-RW-A681 TCGA-RW-A68C TCGA-RW-A68D 
        0.92       108.26         2.93        37.51         6.28        72.79 
TCGA-RW-A8AZ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WT 
        2.89        31.59        36.56        35.51        31.04        42.77 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SR-A6MP 
       27.91        23.21         9.73       114.77       109.25        51.22 
TCGA-SR-A6MY TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HH TCGA-WB-A80K 
       24.66        49.61        13.32        42.48        25.61        41.26 
TCGA-WB-A80L TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A81A TCGA-WB-A81F 
       34.26       127.56        19.59        53.59        24.16        57.11 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81S 
       22.32        24.36        62.04        12.99        23.77 

  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 
            23.90             27.91 
[1] "0.1 - 316.7 (23.9)" "0.9 - 127.6 (27.9)"
[1] "hr=" "2.9"
D37V2, continuous
D37V3, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   81 16
  1P LOSS WILD-TYPE 53 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     81   16
  1P LOSS WILD-TYPE   53   12
                    clus
vv                   1P LOSS MUTATED 1P LOSS WILD-TYPE
  ADRENAL GLAND                   81                53
  EXTRA-ADRENAL SITE              16                12
[1] 2 2
[1] FALSE
D37V4, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   51 46
  1P LOSS WILD-TYPE 37 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     51   46
  1P LOSS WILD-TYPE   37   28
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              51                37
  MALE                46                28
[1] 2 2
[1] FALSE
D37V5, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   91  4
  1P LOSS WILD-TYPE 64  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     91    4
  1P LOSS WILD-TYPE   64    1
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               91                64
  YES               4                 1
[1] 2 2
[1] FALSE
D37V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  1P LOSS MUTATED               9                                             6
  1P LOSS WILD-TYPE             7                                             5
                   vv
clus                PHEOCHROMOCYTOMA
  1P LOSS MUTATED                 82
  1P LOSS WILD-TYPE               53
D37V7, multiclass
                                               clus
vv                                              1P LOSS MUTATED
  PARAGANGLIOMA                                               9
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               6
  PHEOCHROMOCYTOMA                                           82
                                               clus
vv                                              1P LOSS WILD-TYPE
  PARAGANGLIOMA                                                 7
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 5
  PHEOCHROMOCYTOMA                                             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, continuous
                   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    82
  1P LOSS WILD-TYPE                        11    52
D37V9, 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                                         82                52
[1] 4 2
[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    25   0
  1Q LOSS WILD-TYPE 131   6
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               25               137 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                0                 6 
$`1Q LOSS MUTATED`
TCGA-QR-A700 TCGA-QR-A70D TCGA-RW-A68A TCGA-S7-A7WQ TCGA-S7-A7X1 TCGA-WB-A81E 
       32.15         0.23        25.05        26.96        18.94        48.53 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H6 TCGA-QR-A70E TCGA-QR-A70K TCGA-QR-A70X 
        9.93        14.27        15.58         6.31         9.01         6.02 
TCGA-QR-A7IN TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RM-A68T TCGA-RW-A688 
       12.39         0.72         2.30         0.79        77.98         1.22 
TCGA-RX-A8JQ TCGA-SP-A6QF TCGA-SR-A6MT TCGA-W2-A7H7 TCGA-WB-A81D TCGA-WB-A81K 
       20.09        82.62       106.75        17.16        35.84        40.04 
TCGA-WB-A821 
       93.11 

$`1Q LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A70P TCGA-RW-A68B TCGA-RW-A68F 
       58.88        30.51        14.17       117.14        23.90        44.52 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB 
       41.88        13.87        30.51       121.05         3.12        19.86 
TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 
       17.69        74.04        43.07        24.82        10.16        20.19 
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         4.04        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-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H5 TCGA-QR-A702 TCGA-QR-A706 
       19.04         1.05         9.21        31.53         1.28         4.11 
TCGA-QR-A70C TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N 
      116.19         2.33        26.83        29.92        13.12         1.41 
TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       14.20        41.79        17.95        36.23         6.94         1.81 
TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA 
       25.18         4.41        13.08         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        47.64 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A689 TCGA-RW-A68C 
       37.51         1.05         0.85        19.30        27.22         6.28 
TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
       72.79        11.57         2.89        31.59        36.56        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW 
       35.51        31.04        40.70        42.77        27.91        23.21 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       25.32        17.95        24.20         9.73       114.77       109.25 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       79.46       110.04        15.52       111.25         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ 
       51.22        68.61        81.93       110.53        24.66        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        37.35        19.92        13.32        42.48 
TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       20.09         1.18        14.43        18.44        16.60        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       14.79        41.26        34.26         4.47         4.73        25.51 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 
      316.73       127.56        29.16        19.59        53.59        41.23 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       42.35        33.90        24.16        57.11        38.76        63.98 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R 
       22.32        24.36        45.83        62.04        12.99         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 
       23.77        25.51        71.05        78.21       103.17 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.23              0.10 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           106.75            316.73 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            17.16             25.51 
[1] "0.2 - 106.8 (17.2)" "0.1 - 316.7 (25.5)"
[1] "hr="     "8.2e+07"
D38V2, continuous
D38V3, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    19   6
  1Q LOSS WILD-TYPE 115  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     19    6
  1Q LOSS WILD-TYPE  115   22
                    clus
vv                   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ADRENAL GLAND                   19               115
  EXTRA-ADRENAL SITE               6                22
[1] 2 2
[1] FALSE
D38V4, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED   11 14
  1Q LOSS WILD-TYPE 77 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     11   14
  1Q LOSS WILD-TYPE   77   60
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              11                77
  MALE                14                60
[1] 2 2
[1] FALSE
D38V5, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    25   0
  1Q LOSS WILD-TYPE 130   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     25    0
  1Q LOSS WILD-TYPE  130    5
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               25               130
  YES               0                 5
[1] 2 2
[1] FALSE
D38V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  1Q LOSS MUTATED               5                                             1
  1Q LOSS WILD-TYPE            11                                            10
                   vv
clus                PHEOCHROMOCYTOMA
  1Q LOSS MUTATED                 19
  1Q LOSS WILD-TYPE              116
D38V7, multiclass
                                               clus
vv                                              1Q LOSS MUTATED
  PARAGANGLIOMA                                               5
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               1
  PHEOCHROMOCYTOMA                                           19
                                               clus
vv                                              1Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                11
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                10
  PHEOCHROMOCYTOMA                                            116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, continuous
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2                16 
       TCGA-QR-A70P        TCGA-WB-A814        TCGA-WB-A820        TCGA-XG-A823 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-QR-A702        TCGA-QT-A5XJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-QT-A5XP        TCGA-RW-A680        TCGA-RW-A686        TCGA-RW-A8AZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-TT-A6YK        TCGA-WB-A80Q        TCGA-WB-A80Y        TCGA-WB-A81W 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
                   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    18
  1Q LOSS WILD-TYPE                        14   116
D38V9, 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                                         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(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-RW-A68G TCGA-W2-A7HB TCGA-QR-A6GY TCGA-QR-A6H2 TCGA-QR-A70R TCGA-QT-A5XO 
       41.88        19.86         1.05         9.93        14.20         2.30 
TCGA-QT-A69Q TCGA-S7-A7X0 TCGA-WB-A815 TCGA-WB-A821 
        0.79        17.95        53.59        93.11 

$`2P LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU 
       25.05        23.90        44.52        13.87        26.96        30.51 
TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 
       18.94       121.05         3.12        17.69        74.04        43.07 
TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       48.53        24.82        10.16        20.19        31.46        29.03 
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH 
        4.04        17.75         5.88        17.95        81.70        28.08 
TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6H0 
       35.01        23.11         1.25       137.59        19.04         9.21 
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-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-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ 
        1.41        41.79         6.02        12.39        17.95        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        47.64        37.51         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D 
        0.85        19.30         1.22        27.22         6.28        72.79 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
       11.57         2.89        20.09        31.59        36.56        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW 
       35.51        31.04        40.70        42.77        27.91        23.21 
TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       25.32        24.20         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 
       79.46       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-A6MY 
       51.22        68.61        81.93       106.75       110.53        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       26.20        49.61         4.34        37.35        19.92        13.32 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD 
       42.48        20.09        17.16         1.18        14.43        18.44 
TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       16.60        25.61        14.79        41.26        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73        25.51       316.73       127.56        29.16        19.59 
TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F 
       41.23        42.35        33.90        24.16        35.84        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        63.98        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       62.04        12.99         1.61        23.77        25.51        71.05 
TCGA-WB-A81W TCGA-WB-A822 
       78.21       103.17 

  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 
           16.075            25.250 
[1] "0.8 - 93.1 (16.1)"  "0.1 - 316.7 (25.2)"
[1] "hr="     "2.6e+07"
D39V2, continuous
D39V3, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     9   1
  2P LOSS WILD-TYPE 125  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      9    1
  2P LOSS WILD-TYPE  125   27
                    clus
vv                   2P LOSS MUTATED 2P LOSS WILD-TYPE
  ADRENAL GLAND                    9               125
  EXTRA-ADRENAL SITE               1                27
[1] 2 2
[1] FALSE
D39V4, 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
D39V5, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    10   0
  2P LOSS WILD-TYPE 145   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     10    0
  2P LOSS WILD-TYPE  145    5
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               10               145
  YES               0                 5
[1] 2 2
[1] FALSE
D39V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  2P LOSS MUTATED               0                                             1
  2P LOSS WILD-TYPE            16                                            10
                   vv
clus                PHEOCHROMOCYTOMA
  2P LOSS MUTATED                  9
  2P LOSS WILD-TYPE              126
D39V7, multiclass
                                               clus
vv                                              2P LOSS MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               1
  PHEOCHROMOCYTOMA                                            9
                                               clus
vv                                              2P LOSS WILD-TYPE
  PARAGANGLIOMA                                                16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                10
  PHEOCHROMOCYTOMA                                            126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                17 
       TCGA-QR-A70D        TCGA-QR-A70P        TCGA-WB-A814        TCGA-WB-A820 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-XG-A823        TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-QR-A702 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-QT-A5XJ        TCGA-QT-A5XP        TCGA-RW-A680        TCGA-RW-A686 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-RW-A8AZ        TCGA-TT-A6YK        TCGA-WB-A80Q        TCGA-WB-A80Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-WB-A81W 
"2P LOSS WILD-TYPE" 
                   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
D39V9, 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-SR-A6MX TCGA-W2-A7HB TCGA-QR-A6GT TCGA-QR-A6H2 TCGA-QR-A6H6 TCGA-QR-A70K 
        3.12        19.86       137.59         9.93        15.58         9.01 
TCGA-QR-A7IP TCGA-QT-A5XO TCGA-QT-A69Q TCGA-S7-A7X0 TCGA-SP-A6QC TCGA-SP-A6QG 
       17.95         2.30         0.79        17.95       114.77        79.46 
TCGA-WB-A821 
       93.11 

$`2Q LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 
       30.51        18.94       121.05        17.69        74.04        43.07 
TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       48.53        24.82        10.16        20.19        31.46        29.03 
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH 
        4.04        17.75         5.88        17.95        81.70        28.08 
TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 
       35.01        23.11         1.25        19.04         1.05         9.21 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E 
       14.27        31.53         1.28         4.11       116.19         6.31 
TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70R 
        2.33        26.83        29.92        13.12         1.41        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-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        0.72        25.18         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        47.64        37.51         1.05         0.85        19.30 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
        1.22        27.22         6.28        72.79        11.57         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        36.56        37.25        35.51        31.04 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X2 
       40.70        42.77        27.91        23.21        25.32        24.20 
TCGA-SA-A6C2 TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
        9.73       109.25        82.62       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-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
      110.53        24.66        26.20        49.61         4.34        37.35 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       19.92        13.32        42.48        20.09        17.16         1.18 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       14.43        18.44        16.60        25.61        14.79        41.26 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       34.26         4.47         4.73        25.51       316.73       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 
       29.16        19.59        53.59        41.23        42.35        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       24.16        35.84        57.11        38.76        63.98        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R 
       24.36        40.04        45.83        62.04        12.99         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 
       23.77        25.51        71.05        78.21       103.17 

  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 
            17.95             25.32 
[1] "0.8 - 137.6 (17.9)" "0.1 - 316.7 (25.3)"
[1] "hr=" "2.2"
D40V2, continuous
D40V3, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     7   6
  2Q LOSS WILD-TYPE 127  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7    6
  2Q LOSS WILD-TYPE  127   22
                    clus
vv                   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ADRENAL GLAND                    7               127
  EXTRA-ADRENAL SITE               6                22
[1] 2 2
[1] FALSE
D40V4, 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
D40V5, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    13   0
  2Q LOSS WILD-TYPE 142   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     13    0
  2Q LOSS WILD-TYPE  142    5
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               13               142
  YES               0                 5
[1] 2 2
[1] FALSE
D40V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  2Q LOSS MUTATED               4                                             1
  2Q LOSS WILD-TYPE            12                                            10
                   vv
clus                PHEOCHROMOCYTOMA
  2Q LOSS MUTATED                  8
  2Q LOSS WILD-TYPE              127
D40V7, multiclass
                                               clus
vv                                              2Q LOSS MUTATED
  PARAGANGLIOMA                                               4
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               1
  PHEOCHROMOCYTOMA                                            8
                                               clus
vv                                              2Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                12
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                10
  PHEOCHROMOCYTOMA                                            127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V8, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                17 
       TCGA-QR-A70D        TCGA-QR-A70P        TCGA-WB-A814        TCGA-WB-A820 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-XG-A823        TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-QR-A702 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-QT-A5XJ        TCGA-QT-A5XP        TCGA-RW-A680        TCGA-RW-A686 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-RW-A8AZ        TCGA-TT-A6YK        TCGA-WB-A80Q        TCGA-WB-A80Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-WB-A81W 
"2Q LOSS WILD-TYPE" 
                   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
D40V9, 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   58  2
  3P LOSS WILD-TYPE 98  4
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               60               102 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                 4 
$`3P LOSS MUTATED`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        30.51        32.15         0.23       117.14        25.05 
TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-W2-A7HF TCGA-WB-A814 
       13.87        26.96        18.94       121.05        17.69        74.04 
TCGA-WB-A820 TCGA-XG-A823 TCGA-P8-A6RX TCGA-PR-A5PF TCGA-QR-A6GT TCGA-QR-A6GY 
       10.16        20.19        17.75        17.95       137.59         1.05 
TCGA-QR-A6H5 TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A7IN TCGA-QR-A7IP 
       31.53        13.12         1.41        14.20        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XN TCGA-RT-A6Y9 TCGA-RT-A6YA 
       36.23         6.94         1.81        25.18       108.26        50.63 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 
        2.93         7.10        47.64         0.85         1.22        27.22 
TCGA-RW-A68C TCGA-S7-A7WL TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7X0 
        6.28        31.59        31.04        40.70        42.77        17.95 
TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SQ-A6I6 TCGA-SR-A6MT TCGA-SR-A6MU 
      109.25        79.46       110.04         0.10       106.75       110.53 
TCGA-TT-A6YK TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7UY 
       37.35        42.48        20.09        17.16         1.18        14.79 
TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A815 TCGA-WB-A819 TCGA-WB-A81W TCGA-WB-A821 
      316.73        29.16        53.59        33.90        78.21        93.11 

$`3P LOSS WILD-TYPE`
TCGA-QR-A6H1 TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-S7-A7WU TCGA-SR-A6MX 
       14.17        23.90        44.52        41.88        30.51         3.12 
TCGA-W2-A7HB TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-P7-A5NY TCGA-P8-A5KC 
       19.86        43.07        48.53        24.82        31.46        29.03 
TCGA-P8-A5KD TCGA-P8-A6RY TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR 
        4.04         5.88        81.70        28.08        35.01        23.11 
TCGA-QR-A6GS TCGA-QR-A6GX TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H6 
        1.25        19.04         9.21         9.93        14.27        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.28         4.11       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70K TCGA-QR-A70W TCGA-QR-A70X TCGA-QT-A5XM TCGA-QT-A5XO 
       29.92         9.01        41.79         6.02         0.72         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6YC 
        4.41         0.79        13.08        77.98         0.92         8.09 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A686 TCGA-RW-A68D 
       86.89        19.86        37.51         1.05        19.30        72.79 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
       11.57         2.89        20.09        36.56        37.25        35.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       27.91        23.21        25.32        24.20         9.73       114.77 
TCGA-SP-A6QF TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MQ 
       82.62        15.52       111.25         1.41        51.22        68.61 
TCGA-SR-A6MS TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YN 
       81.93        24.66        26.20        49.61         4.34        19.92 
TCGA-TT-A6YO TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-WB-A80K 
       13.32        14.43        18.44        16.60        25.61        41.26 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80Q TCGA-WB-A80Y 
       34.26         4.47         4.73        25.51       127.56        19.59 
TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G 
       41.23        42.35        24.16        35.84        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       63.98        22.32        24.36        40.04        45.83        62.04 
TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A822 
       12.99         1.61        23.77        25.51        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 
            27.09             24.28 
[1] "0.1 - 316.7 (27.1)" "0.7 - 127.6 (24.3)"
[1] "hr=" "1.7"
D41V2, continuous
D41V3, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   47 13
  3P LOSS WILD-TYPE 87 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     47   13
  3P LOSS WILD-TYPE   87   15
                    clus
vv                   3P LOSS MUTATED 3P LOSS WILD-TYPE
  ADRENAL GLAND                   47                87
  EXTRA-ADRENAL SITE              13                15
[1] 2 2
[1] FALSE
D41V4, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   36 24
  3P LOSS WILD-TYPE 52 50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     36   24
  3P LOSS WILD-TYPE   52   50
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              36                52
  MALE                24                50
[1] 2 2
[1] FALSE
D41V5, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   56  3
  3P LOSS WILD-TYPE 99  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     56    3
  3P LOSS WILD-TYPE   99    2
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               56                99
  YES               3                 2
[1] 2 2
[1] FALSE
D41V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  3P LOSS MUTATED               6                                             6
  3P LOSS WILD-TYPE            10                                             5
                   vv
clus                PHEOCHROMOCYTOMA
  3P LOSS MUTATED                 48
  3P LOSS WILD-TYPE               87
D41V7, multiclass
                                               clus
vv                                              3P LOSS MUTATED
  PARAGANGLIOMA                                               6
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               6
  PHEOCHROMOCYTOMA                                           48
                                               clus
vv                                              3P LOSS WILD-TYPE
  PARAGANGLIOMA                                                10
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 5
  PHEOCHROMOCYTOMA                                             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, continuous
                   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                           9    49
  3P LOSS WILD-TYPE                        10    85
D41V9, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      9                10
  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(42) Variable = 3Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED   85  2
  3Q LOSS WILD-TYPE 71  4
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               87                75 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                 4 
$`3Q LOSS MUTATED`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-RW-A68A 
       58.88        30.51        14.17        32.15         0.23        25.05 
TCGA-RW-A68B TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX 
       23.90        13.87        26.96        18.94       121.05         3.12 
TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A820 TCGA-XG-A823 TCGA-P8-A5KD 
       19.86        17.69        74.04        10.16        20.19         4.04 
TCGA-P8-A6RX TCGA-QR-A6GO TCGA-QR-A6GT TCGA-QR-A6H0 TCGA-QR-A6H5 TCGA-QR-A6H6 
       17.75        35.01       137.59         9.21        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A7IN 
        1.28        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-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A685 
      108.26        50.63         2.93         7.10        47.64         0.85 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A7D0 TCGA-S7-A7WL TCGA-S7-A7WP 
        1.22        27.22         6.28        11.57        31.59        31.04 
TCGA-S7-A7WR TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       40.70        17.95        24.20       109.25        82.62        79.46 
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-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK 
      106.75       110.53        24.66        26.20         4.34        37.35 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD 
       42.48        20.09        17.16         1.18        14.43        18.44 
TCGA-W2-A7UY TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A816 
       14.79         4.47         4.73       316.73        29.16        41.23 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81R TCGA-WB-A81T 
       42.35        33.90        57.11        38.76         1.61        25.51 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       78.21        93.11       103.17 

$`3Q LOSS WILD-TYPE`
TCGA-QR-A70P TCGA-RW-A68F TCGA-RW-A68G TCGA-S7-A7WU TCGA-WB-A817 TCGA-WB-A81E 
      117.14        44.52        41.88        30.51        43.07        48.53 
TCGA-WB-A81Q TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       24.82        31.46        29.03         5.88        17.95        81.70 
TCGA-PR-A5PH TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H2 
       28.08        23.11         1.25        19.04         1.05         9.93 
TCGA-QR-A6H3 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
       14.27         4.11       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70K TCGA-QR-A70X TCGA-QT-A5XL TCGA-QT-A5XO TCGA-QT-A69Q 
       29.92         9.01         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-A67W 
       13.08        77.98         0.92         8.09        86.89        19.86 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A686 TCGA-RW-A68D TCGA-RW-A8AZ TCGA-RX-A8JQ 
       37.51         1.05        19.30        72.79         2.89        20.09 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW 
       36.56        37.25        35.51        42.77        27.91        23.21 
TCGA-S7-A7WX TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6N0 
       25.32         9.73       114.77        68.61        81.93        49.61 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7HE TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L 
       19.92        13.32        16.60        25.61        41.26        34.26 
TCGA-WB-A80O TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A81A TCGA-WB-A81D 
       25.51       127.56        19.59        53.59        24.16        35.84 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       63.98        22.32        24.36        40.04        45.83        62.04 
TCGA-WB-A81P TCGA-WB-A81S TCGA-WB-A81V 
       12.99        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 
            24.20             25.51 
[1] "0.1 - 316.7 (24.2)" "0.8 - 127.6 (25.5)"
[1] "hr=" "2.3"
D42V2, continuous
D42V3, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   71 16
  3Q LOSS WILD-TYPE 63 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     71   16
  3Q LOSS WILD-TYPE   63   12
                    clus
vv                   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ADRENAL GLAND                   71                63
  EXTRA-ADRENAL SITE              16                12
[1] 2 2
[1] FALSE
D42V4, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   46 41
  3Q LOSS WILD-TYPE 42 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     46   41
  3Q LOSS WILD-TYPE   42   33
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              46                42
  MALE                41                33
[1] 2 2
[1] FALSE
D42V5, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   82  3
  3Q LOSS WILD-TYPE 73  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     82    3
  3Q LOSS WILD-TYPE   73    2
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               82                73
  YES               3                 2
[1] 2 2
[1] FALSE
D42V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  3Q LOSS MUTATED               8                                             7
  3Q LOSS WILD-TYPE             8                                             4
                   vv
clus                PHEOCHROMOCYTOMA
  3Q LOSS MUTATED                 72
  3Q LOSS WILD-TYPE               63
D42V7, multiclass
                                               clus
vv                                              3Q LOSS MUTATED
  PARAGANGLIOMA                                               8
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               7
  PHEOCHROMOCYTOMA                                           72
                                               clus
vv                                              3Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                 8
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 4
  PHEOCHROMOCYTOMA                                             63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V8, continuous
                   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    71
  3Q LOSS WILD-TYPE                         9    63
D42V9, 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                                         71                63
[1] 4 2
[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-A700 TCGA-QR-A6GS TCGA-QR-A706 TCGA-QR-A70N TCGA-QT-A69Q TCGA-RT-A6YA 
       32.15         1.25         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        42.48        24.36        93.11 

$`4P LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        30.51        14.17         0.23       117.14        25.05 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU 
       23.90        44.52        41.88        13.87        26.96        30.51 
TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 
       18.94       121.05         3.12        19.86        17.69        74.04 
TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY 
       43.07        48.53        24.82        10.16        20.19        31.46 
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       29.03         4.04        17.75         5.88        17.95        81.70 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GY 
       28.08        35.01        23.11       137.59        19.04         1.05 
TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 
        9.21         9.93        14.27        31.53        15.58         1.28 
TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
      116.19         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
        9.01        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        47.64        37.51         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68D TCGA-RW-A7D0 
        0.85        19.30         1.22        27.22        72.79        11.57 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89        20.09        31.59        36.56        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       31.04        40.70        42.77        27.91        23.21        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       17.95        24.20         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 
       79.46       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-A6MY 
       51.22        68.61        81.93       106.75       110.53        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       26.20        49.61         4.34        37.35        19.92        13.32 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       20.09        17.16         1.18        14.43        18.44        16.60 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        14.79        41.26        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 
       25.51       316.73       127.56        29.16        19.59        53.59 
TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F 
       41.23        42.35        33.90        24.16        35.84        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       38.76        63.98        22.32        40.04        45.83        62.04 
TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       12.99         1.61        23.77        25.51        71.05        78.21 
TCGA-WB-A822 
      103.17 

  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             25.18 
[1] "0.8 - 93.1 (6.3)"   "0.1 - 316.7 (25.2)"
[1] "hr="     "2.6e+07"
D43V2, continuous
D43V3, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    10   1
  4P LOSS WILD-TYPE 124  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     10    1
  4P LOSS WILD-TYPE  124   27
                    clus
vv                   4P LOSS MUTATED 4P LOSS WILD-TYPE
  ADRENAL GLAND                   10               124
  EXTRA-ADRENAL SITE               1                27
[1] 2 2
[1] FALSE
D43V4, 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
D43V5, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    11   0
  4P LOSS WILD-TYPE 144   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     11    0
  4P LOSS WILD-TYPE  144    5
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               11               144
  YES               0                 5
[1] 2 2
[1] FALSE
D43V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  4P LOSS MUTATED               1                                             0
  4P LOSS WILD-TYPE            15                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  4P LOSS MUTATED                 10
  4P LOSS WILD-TYPE              125
D43V7, multiclass
                                               clus
vv                                              4P LOSS MUTATED
  PARAGANGLIOMA                                               1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                           10
                                               clus
vv                                              4P LOSS WILD-TYPE
  PARAGANGLIOMA                                                15
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V8, continuous
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                1                17 
       TCGA-QR-A70D        TCGA-QR-A70P        TCGA-WB-A814        TCGA-WB-A820 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-XG-A823        TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-QR-A702 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-QT-A5XJ        TCGA-QT-A5XP        TCGA-RW-A680        TCGA-RW-A686 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-RW-A8AZ        TCGA-TT-A6YK        TCGA-WB-A80Q        TCGA-WB-A80Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-WB-A81W 
"4P LOSS WILD-TYPE" 
                   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
D43V9, 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        42.48        24.36        93.11 

$`4Q LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        30.51        14.17         0.23       117.14        25.05 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU 
       23.90        44.52        41.88        13.87        26.96        30.51 
TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 
       18.94       121.05         3.12        19.86        17.69        74.04 
TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY 
       43.07        48.53        24.82        10.16        20.19        31.46 
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       29.03         4.04        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-A6GX 
       28.08        35.01        23.11         1.25       137.59        19.04 
TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
        1.05         9.21         9.93        14.27        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.28         4.11       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
       29.92        13.12         9.01        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        47.64        37.51 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68D 
        1.05         0.85        19.30         1.22        27.22        72.79 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
       11.57         2.89        20.09        31.59        36.56        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW 
       35.51        31.04        40.70        42.77        27.91        23.21 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       25.32        17.95        24.20         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        79.46       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-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        26.20        49.61         4.34        37.35        19.92 
TCGA-TT-A6YO TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD 
       13.32        20.09        17.16         1.18        14.43        18.44 
TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       16.60        25.61        14.79        41.26        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73        25.51       316.73       127.56        29.16        19.59 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
       53.59        41.23        42.35        33.90        24.16        35.84 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M 
       57.11        38.76        63.98        22.32        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       62.04        12.99         1.61        23.77        25.51        71.05 
TCGA-WB-A81W TCGA-WB-A822 
       78.21       103.17 

  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 
           22.110            25.115 
[1] "0.8 - 93.1 (22.1)"  "0.1 - 316.7 (25.1)"
[1] "hr="     "2.6e+07"
D44V2, continuous
D44V3, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    10   0
  4Q LOSS WILD-TYPE 124  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     10    0
  4Q LOSS WILD-TYPE  124   28
                    clus
vv                   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ADRENAL GLAND                   10               124
  EXTRA-ADRENAL SITE               0                28
[1] 2 2
[1] FALSE
D44V4, 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
D44V5, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    10   0
  4Q LOSS WILD-TYPE 145   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     10    0
  4Q LOSS WILD-TYPE  145    5
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               10               145
  YES               0                 5
[1] 2 2
[1] FALSE
D44V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  4Q LOSS MUTATED               0                                             0
  4Q LOSS WILD-TYPE            16                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  4Q LOSS MUTATED                 10
  4Q LOSS WILD-TYPE              125
D44V7, multiclass
                                               clus
vv                                              4Q LOSS MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                           10
                                               clus
vv                                              4Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, continuous
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                17 
       TCGA-QR-A70D        TCGA-QR-A70P        TCGA-WB-A814        TCGA-WB-A820 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-XG-A823        TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-QR-A702 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-QT-A5XJ        TCGA-QT-A5XP        TCGA-RW-A680        TCGA-RW-A686 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-RW-A8AZ        TCGA-TT-A6YK        TCGA-WB-A80Q        TCGA-WB-A80Y 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-WB-A81W 
"4Q LOSS WILD-TYPE" 
                   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
D44V9, 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        14.79 

$`5P LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 
       74.04        43.07        48.53        24.82        10.16        20.19 
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         4.04        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-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
       19.04         1.05         9.21         9.93        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G 
       15.58         1.28         4.11       116.19         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R 
       26.83        29.92        13.12         9.01         1.41        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        47.64        37.51         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
       19.30         1.22        27.22        72.79        11.57         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        36.56        37.25        35.51        31.04 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       40.70        42.77        27.91        23.21        25.32        17.95 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       24.20         9.73       114.77       109.25        82.62        79.46 
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-A6MY TCGA-SR-A6MZ 
       68.61        81.93       106.75       110.53        24.66        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        37.35        19.92        13.32        42.48 
TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       20.09         1.18        14.43        18.44        16.60        25.61 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       41.26        34.26         4.47         4.73        25.51       316.73 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 
      127.56        29.16        19.59        53.59        41.23        42.35 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       33.90        24.16        35.84        57.11        38.76        63.98 
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        62.04        12.99 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 
        1.61        23.77        25.51        71.05        78.21        93.11 
TCGA-WB-A822 
      103.17 

  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 
            12.39             25.32 
[1] "0.8 - 17.2 (12.4)"  "0.1 - 316.7 (25.3)"
[1] "hr="     "9300000"
D45V2, continuous
D45V3, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     5   0
  5P LOSS WILD-TYPE 129  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5    0
  5P LOSS WILD-TYPE  129   28
                    clus
vv                   5P LOSS MUTATED 5P LOSS WILD-TYPE
  ADRENAL GLAND                    5               129
  EXTRA-ADRENAL SITE               0                28
[1] 2 2
[1] FALSE
D45V4, 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
D45V5, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     5   0
  5P LOSS WILD-TYPE 150   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5    0
  5P LOSS WILD-TYPE  150    5
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                5               150
  YES               0                 5
[1] 2 2
[1] FALSE
D45V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  5P LOSS MUTATED               0                                             0
  5P LOSS WILD-TYPE            16                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  5P LOSS MUTATED                  5
  5P LOSS WILD-TYPE              130
D45V7, multiclass
                                               clus
vv                                              5P LOSS MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                            5
                                               clus
vv                                              5P LOSS WILD-TYPE
  PARAGANGLIOMA                                                16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                17 
       TCGA-QR-A70D        TCGA-QR-A70P        TCGA-WB-A814        TCGA-WB-A820 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-XG-A823        TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-QR-A702 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-QT-A5XJ        TCGA-QT-A5XP        TCGA-RW-A680        TCGA-RW-A686 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-RW-A8AZ        TCGA-TT-A6YK        TCGA-WB-A80Q        TCGA-WB-A80Y 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-WB-A81W 
"5P LOSS WILD-TYPE" 
                   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
D45V9, 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-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 
       74.04        43.07        48.53        24.82        10.16        20.19 
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         4.04        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-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
       19.04         1.05         9.21         9.93        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G 
       15.58         1.28         4.11       116.19         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R 
       26.83        29.92        13.12         9.01         1.41        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 
       47.64        37.51         1.05         0.85        19.30         1.22 
TCGA-RW-A689 TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
       27.22        72.79        11.57         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT 
       36.56        37.25        35.51        31.04        40.70        42.77 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 
       27.91        23.21        25.32        17.95        24.20         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        79.46       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-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      106.75       110.53        24.66        26.20        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       37.35        19.92        13.32        42.48        20.09        17.16 
TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY 
        1.18        14.43        18.44        16.60        25.61        14.79 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       41.26        34.26         4.73        25.51       316.73       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 
       29.16        19.59        53.59        41.23        42.35        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       24.16        35.84        57.11        38.76        63.98        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R 
       24.36        40.04        45.83        62.04        12.99         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A821 TCGA-WB-A822 
       23.77        25.51        71.05        93.11       103.17 

  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             25.18 
[1] "0.8 - 78.2 (7.1)"   "0.1 - 316.7 (25.2)"
[1] "hr="     "2.5e+07"
D46V2, continuous
D46V3, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     7   0
  5Q LOSS WILD-TYPE 127  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7    0
  5Q LOSS WILD-TYPE  127   28
                    clus
vv                   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ADRENAL GLAND                    7               127
  EXTRA-ADRENAL SITE               0                28
[1] 2 2
[1] FALSE
D46V4, 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
D46V5, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     7   0
  5Q LOSS WILD-TYPE 148   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7    0
  5Q LOSS WILD-TYPE  148    5
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                7               148
  YES               0                 5
[1] 2 2
[1] FALSE
D46V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  5Q LOSS MUTATED               0                                             0
  5Q LOSS WILD-TYPE            16                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  5Q LOSS MUTATED                  7
  5Q LOSS WILD-TYPE              128
D46V7, multiclass
                                               clus
vv                                              5Q LOSS MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                            7
                                               clus
vv                                              5Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, continuous
                   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
D46V9, 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    17   1
  6Q LOSS WILD-TYPE 139   5
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               18               144 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                1                 5 
$`6Q LOSS MUTATED`
TCGA-WB-A820 TCGA-XG-A823 TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QR-A70W TCGA-QT-A5XN 
       10.16        20.19        81.70        35.01        41.79        25.18 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WR TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-W2-A7HC 
       36.56        37.25        40.70        24.66         4.34        14.43 
TCGA-W2-A7UY TCGA-WB-A80O TCGA-WB-A80V TCGA-WB-A819 TCGA-WB-A81R TCGA-WB-A81S 
       14.79        25.51        29.16        33.90         1.61        23.77 

$`6Q LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-P7-A5NY TCGA-P8-A5KC 
       74.04        43.07        48.53        24.82        31.46        29.03 
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PH TCGA-QR-A6GR 
        4.04        17.75         5.88        17.95        28.08        23.11 
TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 
        1.25       137.59        19.04         1.05         9.21         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-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-A70R TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ 
        1.41        14.20         6.02        12.39        17.95        36.23 
TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q 
        6.94         1.81         0.72         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        47.64        37.51 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C 
        1.05         0.85        19.30         1.22        27.22         6.28 
TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WO 
       72.79        11.57         2.89        20.09        31.59        35.51 
TCGA-S7-A7WP TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       31.04        42.77        27.91        23.21        25.32        17.95 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       24.20         9.73       114.77       109.25        82.62        79.46 
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-A6MZ TCGA-SR-A6N0 
       68.61        81.93       106.75       110.53        26.20        49.61 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       37.35        19.92        13.32        42.48        20.09        17.16 
TCGA-W2-A7HA TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L 
        1.18        18.44        16.60        25.61        41.26        34.26 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A815 
        4.47         4.73       316.73       127.56        19.59        53.59 
TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G 
       41.23        42.35        24.16        35.84        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       63.98        22.32        24.36        40.04        45.83        62.04 
TCGA-WB-A81P TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       12.99        25.51        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 
           25.345            24.590 
[1] "1.6 - 81.7 (25.3)"  "0.1 - 316.7 (24.6)"
[1] "hr=" "1.8"
D47V2, continuous
D47V3, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    18   0
  6Q LOSS WILD-TYPE 116  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     18    0
  6Q LOSS WILD-TYPE  116   28
                    clus
vv                   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ADRENAL GLAND                   18               116
  EXTRA-ADRENAL SITE               0                28
[1] 2 2
[1] FALSE
D47V4, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   11  7
  6Q LOSS WILD-TYPE 77 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     11    7
  6Q LOSS WILD-TYPE   77   67
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              11                77
  MALE                 7                67
[1] 2 2
[1] FALSE
D47V5, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    18   0
  6Q LOSS WILD-TYPE 137   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     18    0
  6Q LOSS WILD-TYPE  137    5
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               18               137
  YES               0                 5
[1] 2 2
[1] FALSE
D47V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  6Q LOSS MUTATED               0                                             0
  6Q LOSS WILD-TYPE            16                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  6Q LOSS MUTATED                 18
  6Q LOSS WILD-TYPE              117
D47V7, multiclass
                                               clus
vv                                              6Q LOSS MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                           18
                                               clus
vv                                              6Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, continuous
                   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    16
  6Q LOSS WILD-TYPE                        18   118
D47V9, 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                                         16               118
[1] 4 2
[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     6   1
  7Q LOSS WILD-TYPE 150   5
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                7               155 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                 5 
$`7Q LOSS MUTATED`
TCGA-WB-A820 TCGA-QR-A70H TCGA-QT-A5XK TCGA-QT-A5XM TCGA-SP-A6QF TCGA-SR-A6MQ 
       10.16        26.83         6.94         0.72        82.62        68.61 
TCGA-WB-A81N 
       62.04 

$`7Q LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-XG-A823 TCGA-P7-A5NY 
       74.04        43.07        48.53        24.82        20.19        31.46 
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       29.03         4.04        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-A6GX 
       28.08        35.01        23.11         1.25       137.59        19.04 
TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
        1.05         9.21         9.93        14.27        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70I 
        1.28         4.11       116.19         6.31         2.33        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
       13.12         9.01         1.41        14.20        41.79         6.02 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A5XN TCGA-QT-A5XO 
       12.39        17.95        36.23         1.81        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 
       47.64        37.51         1.05         0.85        19.30         1.22 
TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       27.22         6.28        72.79        11.57         2.89        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR 
       31.59        36.56        37.25        35.51        31.04        40.70 
TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 
       42.77        27.91        23.21        25.32        17.95        24.20 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
        9.73       114.77       109.25        79.46       110.04        15.52 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MS TCGA-SR-A6MT 
      111.25         1.41         0.10        51.22        81.93       106.75 
TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
      110.53        24.66        26.20        49.61         4.34        37.35 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       19.92        13.32        42.48        20.09        17.16         1.18 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       14.43        18.44        16.60        25.61        14.79        41.26 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       34.26         4.47         4.73        25.51       316.73       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 
       29.16        19.59        53.59        41.23        42.35        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       24.16        35.84        57.11        38.76        63.98        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S 
       24.36        40.04        45.83        12.99         1.61        23.77 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       25.51        71.05        78.21        93.11       103.17 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.72              0.10 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            82.62            316.73 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            26.83             24.82 
[1] "0.7 - 82.6 (26.8)"  "0.1 - 316.7 (24.8)"
[1] "hr=" "5.6"
D48V2, continuous
D48V3, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     6   1
  7Q LOSS WILD-TYPE 128  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      6    1
  7Q LOSS WILD-TYPE  128   27
                    clus
vv                   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ADRENAL GLAND                    6               128
  EXTRA-ADRENAL SITE               1                27
[1] 2 2
[1] FALSE
D48V4, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    3  4
  7Q LOSS WILD-TYPE 85 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    4
  7Q LOSS WILD-TYPE   85   70
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               3                85
  MALE                 4                70
[1] 2 2
[1] FALSE
D48V5, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     7   0
  7Q LOSS WILD-TYPE 148   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      7    0
  7Q LOSS WILD-TYPE  148    5
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                7               148
  YES               0                 5
[1] 2 2
[1] FALSE
D48V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  7Q LOSS MUTATED               1                                             0
  7Q LOSS WILD-TYPE            15                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  7Q LOSS MUTATED                  6
  7Q LOSS WILD-TYPE              129
D48V7, multiclass
                                               clus
vv                                              7Q LOSS MUTATED
  PARAGANGLIOMA                                               1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                            6
                                               clus
vv                                              7Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                15
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, continuous
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                17 
       TCGA-QR-A70D        TCGA-QR-A70P        TCGA-WB-A814        TCGA-XG-A823 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-QR-A702        TCGA-QT-A5XJ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-QT-A5XP        TCGA-QT-A69Q        TCGA-RW-A680        TCGA-RW-A686 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-RW-A8AZ        TCGA-TT-A6YK        TCGA-WB-A80Q        TCGA-WB-A80Y 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-WB-A81W 
"7Q LOSS WILD-TYPE" 
                   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     4
  7Q LOSS WILD-TYPE                        18   130
D48V9, 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                                          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(49) Variable = 8P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    19   2
  8P LOSS WILD-TYPE 137   4
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               21               141 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                 4 
$`8P LOSS MUTATED`
TCGA-QR-A700 TCGA-RW-A68A TCGA-WB-A81Q TCGA-WB-A820 TCGA-PR-A5PF TCGA-PR-A5PG 
       32.15        25.05        24.82        10.16        17.95        81.70 
TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A70K TCGA-QT-A5XN TCGA-RT-A6YA TCGA-RW-A68D 
      137.59        19.04         9.01        25.18        50.63        72.79 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-SR-A6MT TCGA-W2-A7H5 TCGA-W2-A7HE TCGA-WB-A80V 
       40.70        42.77       106.75        20.09        16.60        29.16 
TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81T 
       12.99         1.61        25.51 

$`8P LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68B 
       58.88        30.51        14.17         0.23       117.14        23.90 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7X1 
       44.52        41.88        13.87        26.96        30.51        18.94 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 
      121.05         3.12        19.86        17.69        74.04        43.07 
TCGA-WB-A81E TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX 
       48.53        20.19        31.46        29.03         4.04        17.75 
TCGA-P8-A6RY TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GY 
        5.88        28.08        35.01        23.11         1.25         1.05 
TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 
        9.21         9.93        14.27        31.53        15.58         1.28 
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-A70J TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
       13.12         1.41        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-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        47.64 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 
       37.51         1.05         0.85        19.30         1.22        27.22 
TCGA-RW-A68C TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        6.28        11.57         2.89        20.09        31.59        36.56 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       37.25        35.51        31.04        27.91        23.21        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       17.95        24.20         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 
       79.46       110.04        15.52       111.25         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ 
       51.22        68.61        81.93       110.53        24.66        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        37.35        19.92        13.32        42.48 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HH TCGA-W2-A7UY 
       17.16         1.18        14.43        18.44        25.61        14.79 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       41.26        34.26         4.47         4.73        25.51       316.73 
TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 
      127.56        19.59        53.59        41.23        42.35        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       24.16        35.84        57.11        38.76        63.98        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        62.04        23.77        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       78.21        93.11       103.17 

  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 
            25.18             24.36 
[1] "1.6 - 137.6 (25.2)" "0.1 - 316.7 (24.4)"
[1] "hr=" "2.7"
D49V2, continuous
D49V3, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    20   1
  8P LOSS WILD-TYPE 114  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     20    1
  8P LOSS WILD-TYPE  114   27
                    clus
vv                   8P LOSS MUTATED 8P LOSS WILD-TYPE
  ADRENAL GLAND                   20               114
  EXTRA-ADRENAL SITE               1                27
[1] 2 2
[1] FALSE
D49V4, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   14  7
  8P LOSS WILD-TYPE 74 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     14    7
  8P LOSS WILD-TYPE   74   67
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              14                74
  MALE                 7                67
[1] 2 2
[1] FALSE
D49V5, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    20   1
  8P LOSS WILD-TYPE 135   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     20    1
  8P LOSS WILD-TYPE  135    4
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               20               135
  YES               1                 4
[1] 2 2
[1] FALSE
D49V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  8P LOSS MUTATED               0                                             0
  8P LOSS WILD-TYPE            16                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  8P LOSS MUTATED                 21
  8P LOSS WILD-TYPE              114
D49V7, multiclass
                                               clus
vv                                              8P LOSS MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                           21
                                               clus
vv                                              8P LOSS WILD-TYPE
  PARAGANGLIOMA                                                16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V8, continuous
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                16 
       TCGA-QR-A70D        TCGA-QR-A70P        TCGA-WB-A814        TCGA-XG-A823 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-PR-A5PH        TCGA-QR-A702        TCGA-QT-A5XJ        TCGA-QT-A5XP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-QT-A69Q        TCGA-RW-A680        TCGA-RW-A686        TCGA-RW-A8AZ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-TT-A6YK        TCGA-WB-A80Q        TCGA-WB-A80Y        TCGA-WB-A81W 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
                   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                           2    18
  8P LOSS WILD-TYPE                        17   116
D49V9, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 4
  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(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-A700 TCGA-RW-A68A TCGA-SR-A6MX TCGA-QR-A6GX TCGA-QR-A70K TCGA-S7-A7WR 
       32.15        25.05         3.12        19.04         9.01        40.70 
TCGA-SR-A6MT TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HD TCGA-WB-A80K TCGA-WB-A80V 
      106.75        20.09        17.16        18.44        41.26        29.16 

$`8Q LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68B 
       58.88        30.51        14.17         0.23       117.14        23.90 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7X1 
       44.52        41.88        13.87        26.96        30.51        18.94 
TCGA-SR-A6MV TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E 
      121.05        19.86        17.69        74.04        43.07        48.53 
TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD 
       24.82        10.16        20.19        31.46        29.03         4.04 
TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO 
       17.75         5.88        17.95        81.70        28.08        35.01 
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 
       23.11         1.25       137.59         1.05         9.21         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-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-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        47.64 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 
       37.51         1.05         0.85        19.30         1.22        27.22 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        6.28        72.79        11.57         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WT TCGA-S7-A7WV 
       36.56        37.25        35.51        31.04        42.77        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       23.21        25.32        17.95        24.20         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        79.46       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-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        26.20        49.61         4.34        37.35        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HE TCGA-W2-A7HH 
       13.32        42.48         1.18        14.43        16.60        25.61 
TCGA-W2-A7UY TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       14.79        34.26         4.47         4.73        25.51       316.73 
TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 
      127.56        19.59        53.59        41.23        42.35        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       24.16        35.84        57.11        38.76        63.98        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R 
       24.36        40.04        45.83        62.04        12.99         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       23.77        25.51        71.05        78.21        93.11       103.17 

  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 
            22.57             25.00 
[1] "3.1 - 106.8 (22.6)" "0.1 - 316.7 (25.0)"
[1] "hr=" "2.9"
D50V2, continuous
D50V3, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    11   1
  8Q LOSS WILD-TYPE 123  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     11    1
  8Q LOSS WILD-TYPE  123   27
                    clus
vv                   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ADRENAL GLAND                   11               123
  EXTRA-ADRENAL SITE               1                27
[1] 2 2
[1] FALSE
D50V4, 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
D50V5, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    12   0
  8Q LOSS WILD-TYPE 143   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     12    0
  8Q LOSS WILD-TYPE  143    5
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               12               143
  YES               0                 5
[1] 2 2
[1] FALSE
D50V6, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                58 
       TCGA-S7-A7WQ        TCGA-S7-A7WU        TCGA-S7-A7X1        TCGA-SR-A6MV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-WB-A817        TCGA-WB-A81E        TCGA-XG-A823        TCGA-P7-A5NY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-PR-A5PF        TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-RT-A6YA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-RT-A6YC        TCGA-RX-A8JQ        TCGA-S7-A7WL        TCGA-S7-A7WM 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-S7-A7WN        TCGA-S7-A7WO        TCGA-S7-A7WP        TCGA-S7-A7WT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-S7-A7WV        TCGA-S7-A7WW        TCGA-S7-A7WX        TCGA-S7-A7X0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-S7-A7X2        TCGA-SP-A6QC        TCGA-SP-A6QD        TCGA-SP-A6QF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SP-A6QG        TCGA-SP-A6QI        TCGA-SP-A6QJ        TCGA-SP-A6QK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SR-A6MQ        TCGA-SR-A6MS        TCGA-SR-A6MY        TCGA-SR-A6MZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SR-A6N0        TCGA-TT-A6YK        TCGA-TT-A6YN        TCGA-TT-A6YO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-TT-A6YP        TCGA-WB-A80L        TCGA-WB-A80Q        TCGA-WB-A815 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-WB-A818        TCGA-WB-A81D        TCGA-WB-A81F        TCGA-WB-A81G 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-WB-A81H        TCGA-WB-A81I        TCGA-WB-A81J        TCGA-WB-A81K 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-WB-A81M        TCGA-WB-A81N        TCGA-WB-A81S        TCGA-WB-A81T 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-WB-A821        TCGA-WB-A822 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  8Q LOSS MUTATED               1                                             0
  8Q LOSS WILD-TYPE            15                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  8Q LOSS MUTATED                 11
  8Q LOSS WILD-TYPE              124
D50V7, multiclass
                                               clus
vv                                              8Q LOSS MUTATED
  PARAGANGLIOMA                                               1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                           11
                                               clus
vv                                              8Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                15
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, continuous
                   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
D50V9, 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-SR-A6MV TCGA-WB-A81Q TCGA-WB-A820 TCGA-QR-A6GO TCGA-QR-A70R TCGA-QR-A7IP 
      121.05        24.82        10.16        35.01        14.20        17.95 
TCGA-QT-A5XP TCGA-RT-A6YA TCGA-SP-A6QJ TCGA-W2-A7H5 TCGA-WB-A81R 
        4.41        50.63        15.52        20.09         1.61 

$`9P LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 
       30.51        18.94         3.12        19.86        17.69        74.04 
TCGA-WB-A817 TCGA-WB-A81E TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD 
       43.07        48.53        20.19        31.46        29.03         4.04 
TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GR 
       17.75         5.88        17.95        81.70        28.08        23.11 
TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 
        1.25       137.59        19.04         1.05         9.21         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-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-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QT-A5XJ TCGA-QT-A5XK 
        1.41        41.79         6.02        12.39        36.23         6.94 
TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A69Q TCGA-QT-A7U0 
        1.81         0.72        25.18         2.30         0.79        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
       77.98         0.92       108.26         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        47.64        37.51         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 
       19.30         1.22        27.22         6.28        72.79        11.57 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89        20.09        31.59        36.56        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       31.04        40.70        42.77        27.91        23.21        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       17.95        24.20         9.73       114.77       109.25        82.62 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
       79.46       110.04       111.25         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ 
       68.61        81.93       106.75       110.53        24.66        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        37.35        19.92        13.32        42.48 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       17.16         1.18        14.43        18.44        16.60        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       14.79        41.26        34.26         4.47         4.73        25.51 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 
      316.73       127.56        29.16        19.59        53.59        41.23 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G 
       42.35        33.90        24.16        35.84        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       63.98        22.32        24.36        40.04        45.83        62.04 
TCGA-WB-A81P TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 
       12.99        23.77        25.51        71.05        78.21        93.11 
TCGA-WB-A822 
      103.17 

  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 
            17.95             25.32 
[1] "1.6 - 121.0 (17.9)" "0.1 - 316.7 (25.3)"
[1] "hr=" "5.9"
D51V2, continuous
D51V3, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     9   2
  9P LOSS WILD-TYPE 125  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      9    2
  9P LOSS WILD-TYPE  125   26
                    clus
vv                   9P LOSS MUTATED 9P LOSS WILD-TYPE
  ADRENAL GLAND                    9               125
  EXTRA-ADRENAL SITE               2                26
[1] 2 2
[1] FALSE
D51V4, 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
D51V5, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     9   2
  9P LOSS WILD-TYPE 146   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      9    2
  9P LOSS WILD-TYPE  146    3
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                9               146
  YES               2                 3
[1] 2 2
[1] FALSE
D51V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  9P LOSS MUTATED               2                                             0
  9P LOSS WILD-TYPE            14                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  9P LOSS MUTATED                  9
  9P LOSS WILD-TYPE              126
D51V7, multiclass
                                               clus
vv                                              9P LOSS MUTATED
  PARAGANGLIOMA                                               2
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                            9
                                               clus
vv                                              9P LOSS WILD-TYPE
  PARAGANGLIOMA                                                14
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V8, continuous
[1] "Remove cluster labels:" "9P LOSS MUTATED"       
clus
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                2                16 
       TCGA-QR-A70D        TCGA-QR-A70P        TCGA-WB-A814        TCGA-XG-A823 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-QR-A702        TCGA-QT-A5XJ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-QT-A69Q        TCGA-RW-A680        TCGA-RW-A686        TCGA-RW-A8AZ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-TT-A6YK        TCGA-WB-A80Q        TCGA-WB-A80Y        TCGA-WB-A81W 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
                   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
D51V9, 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   2
  9Q LOSS WILD-TYPE 146   4
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               12               150 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                2                 4 
$`9Q LOSS MUTATED`
TCGA-SR-A6MV TCGA-WB-A81Q TCGA-WB-A820 TCGA-QR-A6GO TCGA-QR-A70R TCGA-QR-A7IP 
      121.05        24.82        10.16        35.01        14.20        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XP TCGA-RT-A6YA TCGA-SR-A6MP TCGA-W2-A7H5 TCGA-W2-A7H7 
       36.23         4.41        50.63        51.22        20.09        17.16 

$`9Q LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 
       30.51        18.94         3.12        19.86        17.69        74.04 
TCGA-WB-A817 TCGA-WB-A81E TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD 
       43.07        48.53        20.19        31.46        29.03         4.04 
TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GR 
       17.75         5.88        17.95        81.70        28.08        23.11 
TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 
        1.25       137.59        19.04         1.05         9.21         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-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-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QT-A5XK TCGA-QT-A5XL 
        1.41        41.79         6.02        12.39         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-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
        0.92       108.26         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        47.64        37.51         1.05         0.85        19.30 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
        1.22        27.22         6.28        72.79        11.57         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        36.56        37.25        35.51        31.04 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       40.70        42.77        27.91        23.21        25.32        17.95 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       24.20         9.73       114.77       109.25        82.62        79.46 
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-SR-A6N0 
       81.93       106.75       110.53        24.66        26.20        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HA 
        4.34        37.35        19.92        13.32        42.48         1.18 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       14.43        18.44        16.60        25.61        14.79        41.26 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       34.26         4.47         4.73        25.51       316.73       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 
       29.16        19.59        53.59        41.23        42.35        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       24.16        35.84        57.11        38.76        63.98        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R 
       24.36        40.04        45.83        62.04        12.99         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       23.77        25.51        71.05        78.21        93.11       103.17 

  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 
           22.455            25.115 
[1] "4.4 - 121.0 (22.5)" "0.1 - 316.7 (25.1)"
[1] "hr=" "4.7"
D52V2, continuous
D52V3, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    10   2
  9Q LOSS WILD-TYPE 124  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     10    2
  9Q LOSS WILD-TYPE  124   26
                    clus
vv                   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ADRENAL GLAND                   10               124
  EXTRA-ADRENAL SITE               2                26
[1] 2 2
[1] FALSE
D52V4, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    6  6
  9Q LOSS WILD-TYPE 82 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      6    6
  9Q LOSS WILD-TYPE   82   68
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               6                82
  MALE                 6                68
[1] 2 2
[1] FALSE
D52V5, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    10   2
  9Q LOSS WILD-TYPE 145   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     10    2
  9Q LOSS WILD-TYPE  145    3
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               10               145
  YES               2                 3
[1] 2 2
[1] FALSE
D52V6, continuous
[1] "Remove cluster labels:" "9Q LOSS MUTATED"       
clus
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                2                58 
       TCGA-S7-A7WQ        TCGA-S7-A7WU        TCGA-S7-A7X1        TCGA-WB-A817 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-WB-A81E        TCGA-XG-A823        TCGA-P7-A5NY        TCGA-PR-A5PF 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-PR-A5PG        TCGA-PR-A5PH        TCGA-RT-A6YC        TCGA-RX-A8JQ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-S7-A7WL        TCGA-S7-A7WM        TCGA-S7-A7WN        TCGA-S7-A7WO 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-S7-A7WP        TCGA-S7-A7WR        TCGA-S7-A7WT        TCGA-S7-A7WV 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-S7-A7WW        TCGA-S7-A7WX        TCGA-S7-A7X0        TCGA-S7-A7X2 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-SP-A6QC        TCGA-SP-A6QD        TCGA-SP-A6QF        TCGA-SP-A6QG 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-SP-A6QI        TCGA-SP-A6QJ        TCGA-SP-A6QK        TCGA-SR-A6MQ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-SR-A6MS        TCGA-SR-A6MY        TCGA-SR-A6MZ        TCGA-SR-A6N0 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-TT-A6YK        TCGA-TT-A6YN        TCGA-TT-A6YO        TCGA-TT-A6YP 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-WB-A80K        TCGA-WB-A80L        TCGA-WB-A80Q        TCGA-WB-A815 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-WB-A818        TCGA-WB-A81D        TCGA-WB-A81F        TCGA-WB-A81G 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-WB-A81H        TCGA-WB-A81I        TCGA-WB-A81J        TCGA-WB-A81K 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-WB-A81M        TCGA-WB-A81N        TCGA-WB-A81S        TCGA-WB-A81T 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-WB-A821        TCGA-WB-A822 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  9Q LOSS MUTATED               2                                             0
  9Q LOSS WILD-TYPE            14                                            11
                   vv
clus                PHEOCHROMOCYTOMA
  9Q LOSS MUTATED                 10
  9Q LOSS WILD-TYPE              125
D52V7, multiclass
                                               clus
vv                                              9Q LOSS MUTATED
  PARAGANGLIOMA                                               2
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               0
  PHEOCHROMOCYTOMA                                           10
                                               clus
vv                                              9Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                14
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                11
  PHEOCHROMOCYTOMA                                            125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V8, continuous
                   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    10
  9Q LOSS WILD-TYPE                        17   124
D52V9, 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                                         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(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-QR-A6GU TCGA-QR-A6GZ TCGA-RW-A68A TCGA-RW-A68F TCGA-RW-A7CZ TCGA-S7-A7WQ 
       58.88        30.51        25.05        44.52        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-XG-A823 TCGA-P8-A6RX TCGA-P8-A6RY TCGA-QR-A6H2 
       30.51        18.94        20.19        17.75         5.88         9.93 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70J TCGA-QR-A70K 
       31.53        15.58         1.28         4.11        13.12         9.01 
TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A7U0 TCGA-RM-A68T 
        1.41        14.20        12.39        17.95        13.08        77.98 
TCGA-RM-A68W TCGA-RT-A6YA TCGA-RW-A67X TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A68C 
        0.92        50.63         2.93        37.51         1.05         6.28 
TCGA-RW-A8AZ TCGA-S7-A7WP TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-SP-A6QD TCGA-SR-A6MT 
        2.89        31.04        23.21        17.95       109.25       106.75 
TCGA-SR-A6MU TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7UY 
      110.53        49.61        37.35        42.48        17.16        14.79 
TCGA-WB-A80M TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M 
        4.47        53.59        41.23        22.32        40.04        45.83 
TCGA-WB-A81P TCGA-WB-A81S TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       12.99        23.77        71.05        78.21        93.11       103.17 

$`11P LOSS WILD-TYPE`
TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68B TCGA-RW-A68G 
       14.17        32.15         0.23       117.14        23.90        41.88 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 
      121.05         3.12        19.86        17.69        74.04        43.07 
TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD 
       48.53        24.82        10.16        31.46        29.03         4.04 
TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS 
       17.95        81.70        28.08        35.01        23.11         1.25 
TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H3 TCGA-QR-A70C 
      137.59        19.04         1.05         9.21        14.27       116.19 
TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70W TCGA-QR-A70X 
        6.31         2.33        26.83        29.92        41.79         6.02 
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-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        4.41         0.79       108.26         8.09        86.89        19.86 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 
        7.10        47.64         0.85        19.30         1.22        27.22 
TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
       72.79        11.57        20.09        31.59        36.56        37.25 
TCGA-S7-A7WO TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X2 
       35.51        40.70        42.77        27.91        25.32        24.20 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
        9.73       114.77        82.62        79.46       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-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7H5 
       24.66        26.20         4.34        19.92        13.32        20.09 
TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-WB-A80K 
        1.18        14.43        18.44        16.60        25.61        41.26 
TCGA-WB-A80L TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
       34.26         4.73        25.51       316.73       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F 
       19.59        42.35        33.90        24.16        35.84        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81J TCGA-WB-A81N TCGA-WB-A81R TCGA-WB-A81T 
       38.76        63.98        24.36        62.04         1.61        25.51 

  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 
            22.765             25.415 
[1] "0.9 - 110.5 (22.8)" "0.1 - 316.7 (25.4)"
[1] "hr=" "1.9"
D53V2, continuous
D53V3, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   43 11
  11P LOSS WILD-TYPE 91 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     43   11
  11P LOSS WILD-TYPE   91   17
                    clus
vv                   11P LOSS MUTATED 11P LOSS WILD-TYPE
  ADRENAL GLAND                    43                 91
  EXTRA-ADRENAL SITE               11                 17
[1] 2 2
[1] FALSE
D53V4, 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
D53V5, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    53   1
  11P LOSS WILD-TYPE 102   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     53    1
  11P LOSS WILD-TYPE  102    4
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                53                102
  YES                1                  4
[1] 2 2
[1] FALSE
D53V6, continuous
                    vv
clus                 PARAGANGLIOMA
  11P LOSS MUTATED               6
  11P LOSS WILD-TYPE            10
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  11P LOSS MUTATED                                               5
  11P LOSS WILD-TYPE                                             6
                    vv
clus                 PHEOCHROMOCYTOMA
  11P LOSS MUTATED                 43
  11P LOSS WILD-TYPE               92
D53V7, multiclass
                                               clus
vv                                              11P LOSS MUTATED
  PARAGANGLIOMA                                                6
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                5
  PHEOCHROMOCYTOMA                                            43
                                               clus
vv                                              11P LOSS WILD-TYPE
  PARAGANGLIOMA                                                 10
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                  6
  PHEOCHROMOCYTOMA                                              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V8, continuous
                    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
D53V9, 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-QR-A6GU TCGA-QR-A6GZ TCGA-RW-A68F TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU 
       58.88        30.51        44.52        13.87        26.96        30.51 
TCGA-S7-A7X1 TCGA-XG-A823 TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-QR-A6GS 
       18.94        20.19        17.75         5.88        17.95         1.25 
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        37.51 
TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A8AZ TCGA-S7-A7WP TCGA-S7-A7WW TCGA-S7-A7X0 
       27.22         6.28         2.89        31.04        23.21        17.95 
TCGA-SR-A6MT TCGA-SR-A6N0 TCGA-TT-A6YP TCGA-W2-A7UY TCGA-WB-A815 TCGA-WB-A81P 
      106.75        49.61        42.48        14.79        53.59        12.99 
TCGA-WB-A81S TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 
       23.77        71.05        78.21        93.11 

$`11Q LOSS WILD-TYPE`
TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A TCGA-RW-A68B 
       14.17        32.15         0.23       117.14        25.05        23.90 
TCGA-RW-A68G TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 
       41.88       121.05         3.12        19.86        17.69        74.04 
TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-P7-A5NY TCGA-P8-A5KC 
       43.07        48.53        24.82        10.16        31.46        29.03 
TCGA-P8-A5KD TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GT 
        4.04        81.70        28.08        35.01        23.11       137.59 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H3 TCGA-QR-A6H6 TCGA-QR-A702 
       19.04         1.05         9.21        14.27        15.58         1.28 
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-A70J TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IP 
       13.12         9.01        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        47.64 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68D TCGA-RW-A7D0 
        1.05         0.85        19.30         1.22        72.79        11.57 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WR 
       20.09        31.59        36.56        37.25        35.51        40.70 
TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       42.77        27.91        25.32        24.20         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        79.46       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-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       24.66        26.20         4.34        37.35        19.92        13.32 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       20.09        17.16         1.18        14.43        18.44        16.60 
TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       25.61        41.26        34.26         4.47         4.73        25.51 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A816 TCGA-WB-A818 
      316.73       127.56        29.16        19.59        41.23        42.35 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       33.90        24.16        35.84        57.11        38.76        63.98 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81R 
       22.32        24.36        40.04        45.83        62.04         1.61 
TCGA-WB-A81T TCGA-WB-A822 
       25.51       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 
             21.70              25.25 
[1] "0.8 - 106.8 (21.7)" "0.1 - 316.7 (25.2)"
[1] "hr=" "1.2"
D54V2, continuous
D54V3, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   35  5
  11Q LOSS WILD-TYPE 99 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     35    5
  11Q LOSS WILD-TYPE   99   23
                    clus
vv                   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ADRENAL GLAND                    35                 99
  EXTRA-ADRENAL SITE                5                 23
[1] 2 2
[1] FALSE
D54V4, 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
D54V5, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    40   0
  11Q LOSS WILD-TYPE 115   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     40    0
  11Q LOSS WILD-TYPE  115    5
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                40                115
  YES                0                  5
[1] 2 2
[1] FALSE
D54V6, continuous
                    vv
clus                 PARAGANGLIOMA
  11Q LOSS MUTATED               2
  11Q LOSS WILD-TYPE            14
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  11Q LOSS MUTATED                                               3
  11Q LOSS WILD-TYPE                                             8
                    vv
clus                 PHEOCHROMOCYTOMA
  11Q LOSS MUTATED                 35
  11Q LOSS WILD-TYPE              100
D54V7, multiclass
                                               clus
vv                                              11Q LOSS MUTATED
  PARAGANGLIOMA                                                2
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                3
  PHEOCHROMOCYTOMA                                            35
                                               clus
vv                                              11Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                 14
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                  8
  PHEOCHROMOCYTOMA                                             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V8, continuous
                    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
D54V9, 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 = 12P LOSS MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED     2   1
  12P LOSS WILD-TYPE 154   5
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                159 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                  5 
$`12P LOSS MUTATED`
TCGA-PR-A5PF TCGA-RW-A8AZ TCGA-SP-A6QJ 
       17.95         2.89        15.52 

$`12P LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 
       74.04        43.07        48.53        24.82        10.16        20.19 
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG 
       31.46        29.03         4.04        17.75         5.88        81.70 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX 
       28.08        35.01        23.11         1.25       137.59        19.04 
TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
        1.05         9.21         9.93        14.27        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.28         4.11       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W 
       29.92        13.12         9.01         1.41        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        47.64        37.51         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D 
        0.85        19.30         1.22        27.22         6.28        72.79 
TCGA-RW-A7D0 TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
       11.57        20.09        31.59        36.56        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       31.04        40.70        42.77        27.91        23.21        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       17.95        24.20         9.73       114.77       109.25        82.62 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
       79.46       110.04       111.25         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ 
       68.61        81.93       106.75       110.53        24.66        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        37.35        19.92        13.32        42.48 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       20.09        17.16         1.18        14.43        18.44        16.60 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        14.79        41.26        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 
       25.51       316.73       127.56        29.16        19.59        53.59 
TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F 
       41.23        42.35        33.90        24.16        35.84        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        63.98        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       62.04        12.99         1.61        23.77        25.51        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       78.21        93.11       103.17 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              2.89               0.10 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             17.95             316.73 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             15.52              25.18 
[1] "2.9 - 17.9 (15.5)"  "0.1 - 316.7 (25.2)"
[1] "hr=" "29" 
D55V2, continuous
D55V3, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     3   0
  12P LOSS WILD-TYPE 131  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    0
  12P LOSS WILD-TYPE  131   28
                    clus
vv                   12P LOSS MUTATED 12P LOSS WILD-TYPE
  ADRENAL GLAND                     3                131
  EXTRA-ADRENAL SITE                0                 28
[1] 2 2
[1] FALSE
D55V4, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    2  1
  12P LOSS WILD-TYPE 86 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2    1
  12P LOSS WILD-TYPE   86   73
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                2                 86
  MALE                  1                 73
[1] 2 2
[1] FALSE
D55V5, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     3   0
  12P LOSS WILD-TYPE 152   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    0
  12P LOSS WILD-TYPE  152    5
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 3                152
  YES                0                  5
[1] 2 2
[1] FALSE
D55V6, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                 58 
        TCGA-S7-A7WQ         TCGA-S7-A7WU         TCGA-S7-A7X1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SR-A6MV         TCGA-WB-A817         TCGA-WB-A81E 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-XG-A823         TCGA-P7-A5NY         TCGA-PR-A5PG 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-PR-A5PH         TCGA-RT-A6YA         TCGA-RT-A6YC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-RX-A8JQ         TCGA-S7-A7WL         TCGA-S7-A7WM 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-S7-A7WN         TCGA-S7-A7WO         TCGA-S7-A7WP 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-S7-A7WR         TCGA-S7-A7WT         TCGA-S7-A7WV 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-S7-A7WW         TCGA-S7-A7WX         TCGA-S7-A7X0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-S7-A7X2         TCGA-SP-A6QC         TCGA-SP-A6QD 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SP-A6QF         TCGA-SP-A6QG         TCGA-SP-A6QI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SP-A6QK         TCGA-SR-A6MQ         TCGA-SR-A6MS 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SR-A6MY         TCGA-SR-A6MZ         TCGA-SR-A6N0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-TT-A6YK         TCGA-TT-A6YN         TCGA-TT-A6YO 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-TT-A6YP         TCGA-WB-A80K         TCGA-WB-A80L 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-WB-A80Q         TCGA-WB-A815         TCGA-WB-A818 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-WB-A81D         TCGA-WB-A81F         TCGA-WB-A81G 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-WB-A81H         TCGA-WB-A81I         TCGA-WB-A81J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-WB-A81K         TCGA-WB-A81M         TCGA-WB-A81N 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-WB-A81S         TCGA-WB-A81T         TCGA-WB-A821 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-WB-A822 
"12P LOSS WILD-TYPE" 
                    vv
clus                 PARAGANGLIOMA
  12P LOSS MUTATED               0
  12P LOSS WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  12P LOSS MUTATED                                               0
  12P LOSS WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  12P LOSS MUTATED                  3
  12P LOSS WILD-TYPE              132
D55V7, multiclass
                                               clus
vv                                              12P LOSS MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                             3
                                               clus
vv                                              12P LOSS WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             132
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V8, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 17 
        TCGA-QR-A70D         TCGA-QR-A70P         TCGA-WB-A814 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-WB-A820         TCGA-XG-A823         TCGA-PR-A5PG 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-PR-A5PH         TCGA-QR-A702         TCGA-QT-A5XJ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-QT-A5XP         TCGA-QT-A69Q         TCGA-RW-A680 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-RW-A686         TCGA-TT-A6YK         TCGA-WB-A80Q 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-WB-A80Y         TCGA-WB-A81W 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     0
  12P LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                           0     3
  12P LOSS WILD-TYPE                        19   131
D55V9, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P 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(56) Variable = 13Q LOSS MUTATION ANALYSIS
D56V1, 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-QR-A700 TCGA-RW-A68A TCGA-PR-A5PF TCGA-QR-A70R TCGA-QT-A5XP TCGA-S7-A7WX 
       32.15        25.05        17.95        14.20         4.41        25.32 
TCGA-SP-A6QF TCGA-W2-A7H5 
       82.62        20.09 

$`13Q LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68B 
       58.88        30.51        14.17         0.23       117.14        23.90 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7X1 
       44.52        41.88        13.87        26.96        30.51        18.94 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 
      121.05         3.12        19.86        17.69        74.04        43.07 
TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       48.53        24.82        10.16        20.19        31.46        29.03 
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO 
        4.04        17.75         5.88        81.70        28.08        35.01 
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 
       23.11         1.25       137.59        19.04         1.05         9.21 
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-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
      116.19         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
        9.01         1.41        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-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        47.64 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 
       37.51         1.05         0.85        19.30         1.22        27.22 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        6.28        72.79        11.57         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT 
       36.56        37.25        35.51        31.04        40.70        42.77 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       27.91        23.21        17.95        24.20         9.73       114.77 
TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
      109.25        79.46       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-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        26.20        49.61         4.34        37.35        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD 
       13.32        42.48        17.16         1.18        14.43        18.44 
TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       16.60        25.61        14.79        41.26        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73        25.51       316.73       127.56        29.16        19.59 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
       53.59        41.23        42.35        33.90        24.16        35.84 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       57.11        38.76        63.98        22.32        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       45.83        62.04        12.99         1.61        23.77        25.51 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       71.05        78.21        93.11       103.17 

  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 
             22.57              25.00 
[1] "4.4 - 82.6 (22.6)"  "0.1 - 316.7 (25.0)"
[1] "hr="     "2.6e+07"
D56V2, continuous
D56V3, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     8   0
  13Q LOSS WILD-TYPE 126  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8    0
  13Q LOSS WILD-TYPE  126   28
                    clus
vv                   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ADRENAL GLAND                     8                126
  EXTRA-ADRENAL SITE                0                 28
[1] 2 2
[1] FALSE
D56V4, 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
D56V5, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     8   0
  13Q LOSS WILD-TYPE 147   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8    0
  13Q LOSS WILD-TYPE  147    5
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 8                147
  YES                0                  5
[1] 2 2
[1] FALSE
D56V6, continuous
                    vv
clus                 PARAGANGLIOMA
  13Q LOSS MUTATED               0
  13Q LOSS WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  13Q LOSS MUTATED                                               0
  13Q LOSS WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  13Q LOSS MUTATED                  8
  13Q LOSS WILD-TYPE              127
D56V7, multiclass
                                               clus
vv                                              13Q LOSS MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                             8
                                               clus
vv                                              13Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V8, continuous
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                 17 
        TCGA-QR-A70D         TCGA-QR-A70P         TCGA-WB-A814 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-WB-A820         TCGA-XG-A823         TCGA-PR-A5PG 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-PR-A5PH         TCGA-QR-A702         TCGA-QT-A5XJ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-QT-A69Q         TCGA-RW-A680         TCGA-RW-A686 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-RW-A8AZ         TCGA-TT-A6YK         TCGA-WB-A80Q 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-WB-A80Y         TCGA-WB-A81W 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
                    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
D56V9, 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(57) Variable = 14Q LOSS MUTATION ANALYSIS
D57V1, 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-SR-A6MV TCGA-W2-A7HF TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A70H TCGA-QR-A70R 
      121.05        17.69        28.08        35.01        26.83        14.20 
TCGA-QR-A7IP TCGA-QT-A69Q TCGA-RT-A6YA TCGA-RW-A67X TCGA-RW-A689 TCGA-RW-A68C 
       17.95         0.79        50.63         2.93        27.22         6.28 
TCGA-S7-A7WR TCGA-S7-A7WV TCGA-SR-A6MS TCGA-W2-A7H5 TCGA-WB-A815 TCGA-WB-A81K 
       40.70        27.91        81.93        20.09        53.59        40.04 
TCGA-WB-A81S TCGA-WB-A821 
       23.77        93.11 

$`14Q LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MX TCGA-W2-A7HB TCGA-WB-A814 TCGA-WB-A817 
       30.51        18.94         3.12        19.86        74.04        43.07 
TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       48.53        24.82        10.16        20.19        31.46        29.03 
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-QR-A6GR 
        4.04        17.75         5.88        17.95        81.70        23.11 
TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 
        1.25       137.59        19.04         1.05         9.21         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-A70E TCGA-QR-A70G TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N 
        6.31         2.33        29.92        13.12         9.01         1.41 
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-A7U0 TCGA-RM-A68T 
        0.72        25.18         2.30         4.41        13.08        77.98 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67Y 
        0.92       108.26         8.09        86.89        19.86         7.10 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
       47.64        37.51         1.05         0.85        19.30         1.22 
TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
       72.79        11.57         2.89        20.09        31.59        36.56 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WT TCGA-S7-A7WW TCGA-S7-A7WX 
       37.25        35.51        31.04        42.77        23.21        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       17.95        24.20         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 
       79.46       110.04        15.52       111.25         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ 
       51.22        68.61       106.75       110.53        24.66        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        37.35        19.92        13.32        42.48 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       17.16         1.18        14.43        18.44        16.60        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       14.79        41.26        34.26         4.47         4.73        25.51 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A816 TCGA-WB-A818 
      316.73       127.56        29.16        19.59        41.23        42.35 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       33.90        24.16        35.84        57.11        38.76        63.98 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R 
       22.32        24.36        45.83        62.04        12.99         1.61 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 
       25.51        71.05        78.21       103.17 

  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 
            27.565             24.510 
[1] "0.8 - 121.0 (27.6)" "0.1 - 316.7 (24.5)"
[1] "hr="     "8.6e+07"
D57V2, continuous
D57V3, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    18   2
  14Q LOSS WILD-TYPE 116  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     18    2
  14Q LOSS WILD-TYPE  116   26
                    clus
vv                   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ADRENAL GLAND                    18                116
  EXTRA-ADRENAL SITE                2                 26
[1] 2 2
[1] FALSE
D57V4, 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
D57V5, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    19   1
  14Q LOSS WILD-TYPE 136   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     19    1
  14Q LOSS WILD-TYPE  136    4
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                19                136
  YES                1                  4
[1] 2 2
[1] FALSE
D57V6, continuous
                    vv
clus                 PARAGANGLIOMA
  14Q LOSS MUTATED               2
  14Q LOSS WILD-TYPE            14
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  14Q LOSS MUTATED                                               0
  14Q LOSS WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  14Q LOSS MUTATED                 18
  14Q LOSS WILD-TYPE              117
D57V7, multiclass
                                               clus
vv                                              14Q LOSS MUTATED
  PARAGANGLIOMA                                                2
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                            18
                                               clus
vv                                              14Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                 14
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V8, continuous
[1] "Remove cluster labels:" "14Q LOSS MUTATED"      
clus
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 2                 16 
        TCGA-QR-A70D         TCGA-QR-A70P         TCGA-WB-A814 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-WB-A820         TCGA-XG-A823         TCGA-PR-A5PG 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-QR-A702         TCGA-QT-A5XJ         TCGA-QT-A5XP 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-RW-A680         TCGA-RW-A686         TCGA-RW-A8AZ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-TT-A6YK         TCGA-WB-A80Q         TCGA-WB-A80Y 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-WB-A81W 
"14Q LOSS WILD-TYPE" 
                    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
D57V9, 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(58) Variable = 15Q LOSS MUTATION ANALYSIS
D58V1, 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-A6MV TCGA-W2-A7HF TCGA-SR-A6MQ 
      121.05        17.69        68.61 

$`15Q LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MX TCGA-W2-A7HB TCGA-WB-A814 TCGA-WB-A817 
       30.51        18.94         3.12        19.86        74.04        43.07 
TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       48.53        24.82        10.16        20.19        31.46        29.03 
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH 
        4.04        17.75         5.88        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-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 
        9.21         9.93        14.27        31.53        15.58         1.28 
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-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
       13.12         9.01         1.41        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        47.64        37.51         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 
       19.30         1.22        27.22         6.28        72.79        11.57 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89        20.09        31.59        36.56        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       31.04        40.70        42.77        27.91        23.21        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       17.95        24.20         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 
       79.46       110.04        15.52       111.25         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ 
       51.22        81.93       106.75       110.53        24.66        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        37.35        19.92        13.32        42.48 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       20.09        17.16         1.18        14.43        18.44        16.60 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        14.79        41.26        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 
       25.51       316.73       127.56        29.16        19.59        53.59 
TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F 
       41.23        42.35        33.90        24.16        35.84        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        63.98        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       62.04        12.99         1.61        23.77        25.51        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       78.21        93.11       103.17 

  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              24.82 
[1] "17.7 - 121.0 (68.6)" "0.1 - 316.7 (24.8)" 
[1] "hr="     "3.1e+07"
D58V2, continuous
D58V3, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     1   2
  15Q LOSS WILD-TYPE 133  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    2
  15Q LOSS WILD-TYPE  133   26
                    clus
vv                   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ADRENAL GLAND                     1                133
  EXTRA-ADRENAL SITE                2                 26
[1] 2 2
[1] FALSE
D58V4, 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
D58V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     2   1
  15Q LOSS WILD-TYPE 153   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2    1
  15Q LOSS WILD-TYPE  153    4
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 2                153
  YES                1                  4
[1] 2 2
[1] FALSE
D58V6, continuous
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                 58 
        TCGA-S7-A7WQ         TCGA-S7-A7WU         TCGA-S7-A7X1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-WB-A817         TCGA-WB-A81E         TCGA-XG-A823 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-P7-A5NY         TCGA-PR-A5PF         TCGA-PR-A5PG 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-PR-A5PH         TCGA-RT-A6YA         TCGA-RT-A6YC 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-RX-A8JQ         TCGA-S7-A7WL         TCGA-S7-A7WM 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-S7-A7WN         TCGA-S7-A7WO         TCGA-S7-A7WP 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-S7-A7WR         TCGA-S7-A7WT         TCGA-S7-A7WV 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-S7-A7WW         TCGA-S7-A7WX         TCGA-S7-A7X0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-S7-A7X2         TCGA-SP-A6QC         TCGA-SP-A6QD 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-SP-A6QF         TCGA-SP-A6QG         TCGA-SP-A6QI 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-SP-A6QJ         TCGA-SP-A6QK         TCGA-SR-A6MS 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-SR-A6MY         TCGA-SR-A6MZ         TCGA-SR-A6N0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-TT-A6YK         TCGA-TT-A6YN         TCGA-TT-A6YO 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-TT-A6YP         TCGA-WB-A80K         TCGA-WB-A80L 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-WB-A80Q         TCGA-WB-A815         TCGA-WB-A818 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-WB-A81D         TCGA-WB-A81F         TCGA-WB-A81G 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-WB-A81H         TCGA-WB-A81I         TCGA-WB-A81J 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-WB-A81K         TCGA-WB-A81M         TCGA-WB-A81N 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-WB-A81S         TCGA-WB-A81T         TCGA-WB-A821 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-WB-A822 
"15Q LOSS WILD-TYPE" 
                    vv
clus                 PARAGANGLIOMA
  15Q LOSS MUTATED               2
  15Q LOSS WILD-TYPE            14
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  15Q LOSS MUTATED                                               0
  15Q LOSS WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  15Q LOSS MUTATED                  1
  15Q LOSS WILD-TYPE              134
D58V7, multiclass
                                               clus
vv                                              15Q LOSS MUTATED
  PARAGANGLIOMA                                                2
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                             1
                                               clus
vv                                              15Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                 14
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V8, continuous
                    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
D58V9, 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(59) Variable = 16P LOSS MUTATION ANALYSIS
D59V1, 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-QR-A700 TCGA-QR-A70P TCGA-SR-A6MX TCGA-WB-A81Q TCGA-PR-A5PF TCGA-QR-A70K 
       32.15       117.14         3.12        24.82        17.95         9.01 
TCGA-QT-A69Q TCGA-SR-A6MT TCGA-WB-A81S 
        0.79       106.75        23.77 

$`16P LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A70D TCGA-RW-A68A TCGA-RW-A68B 
       58.88        30.51        14.17         0.23        25.05        23.90 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7X1 
       44.52        41.88        13.87        26.96        30.51        18.94 
TCGA-SR-A6MV TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E 
      121.05        19.86        17.69        74.04        43.07        48.53 
TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX 
       10.16        20.19        31.46        29.03         4.04        17.75 
TCGA-P8-A6RY TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS 
        5.88        81.70        28.08        35.01        23.11         1.25 
TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 
      137.59        19.04         1.05         9.21         9.93        14.27 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E 
       31.53        15.58         1.28         4.11       116.19         6.31 
TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70R 
        2.33        26.83        29.92        13.12         1.41        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-A7U0 
        1.81         0.72        25.18         2.30         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        47.64        37.51         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D 
        0.85        19.30         1.22        27.22         6.28        72.79 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
       11.57         2.89        20.09        31.59        36.56        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW 
       35.51        31.04        40.70        42.77        27.91        23.21 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       25.32        17.95        24.20         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        79.46       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-A6MY 
        0.10        51.22        68.61        81.93       110.53        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       26.20        49.61         4.34        37.35        19.92        13.32 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD 
       42.48        20.09        17.16         1.18        14.43        18.44 
TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       16.60        25.61        14.79        41.26        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73        25.51       316.73       127.56        29.16        19.59 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
       53.59        41.23        42.35        33.90        24.16        35.84 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       57.11        38.76        63.98        22.32        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V 
       45.83        62.04        12.99         1.61        25.51        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       78.21        93.11       103.17 

  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              25.18 
[1] "0.8 - 117.1 (23.8)" "0.1 - 316.7 (25.2)"
[1] "hr=" "15" 
D59V2, continuous
D59V3, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     7   2
  16P LOSS WILD-TYPE 127  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7    2
  16P LOSS WILD-TYPE  127   26
                    clus
vv                   16P LOSS MUTATED 16P LOSS WILD-TYPE
  ADRENAL GLAND                     7                127
  EXTRA-ADRENAL SITE                2                 26
[1] 2 2
[1] FALSE
D59V4, 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
D59V5, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     7   2
  16P LOSS WILD-TYPE 148   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7    2
  16P LOSS WILD-TYPE  148    3
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 7                148
  YES                2                  3
[1] 2 2
[1] FALSE
D59V6, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 58 
        TCGA-S7-A7WQ         TCGA-S7-A7WU         TCGA-S7-A7X1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SR-A6MV         TCGA-WB-A817         TCGA-WB-A81E 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-XG-A823         TCGA-P7-A5NY         TCGA-PR-A5PG 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-PR-A5PH         TCGA-RT-A6YA         TCGA-RT-A6YC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-RX-A8JQ         TCGA-S7-A7WL         TCGA-S7-A7WM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-S7-A7WN         TCGA-S7-A7WO         TCGA-S7-A7WP 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-S7-A7WR         TCGA-S7-A7WT         TCGA-S7-A7WV 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-S7-A7WW         TCGA-S7-A7WX         TCGA-S7-A7X0 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-S7-A7X2         TCGA-SP-A6QC         TCGA-SP-A6QD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SP-A6QF         TCGA-SP-A6QG         TCGA-SP-A6QI 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SP-A6QJ         TCGA-SP-A6QK         TCGA-SR-A6MQ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SR-A6MS         TCGA-SR-A6MY         TCGA-SR-A6MZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SR-A6N0         TCGA-TT-A6YK         TCGA-TT-A6YN 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-TT-A6YO         TCGA-TT-A6YP         TCGA-WB-A80K 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-WB-A80L         TCGA-WB-A80Q         TCGA-WB-A815 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-WB-A818         TCGA-WB-A81D         TCGA-WB-A81F 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-WB-A81G         TCGA-WB-A81H         TCGA-WB-A81I 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-WB-A81J         TCGA-WB-A81K         TCGA-WB-A81M 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-WB-A81N         TCGA-WB-A81T         TCGA-WB-A821 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-WB-A822 
"16P LOSS WILD-TYPE" 
                    vv
clus                 PARAGANGLIOMA
  16P LOSS MUTATED               2
  16P LOSS WILD-TYPE            14
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  16P LOSS MUTATED                                               0
  16P LOSS WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  16P LOSS MUTATED                  7
  16P LOSS WILD-TYPE              128
D59V7, multiclass
                                               clus
vv                                              16P LOSS MUTATED
  PARAGANGLIOMA                                                2
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                             7
                                               clus
vv                                              16P LOSS WILD-TYPE
  PARAGANGLIOMA                                                 14
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V8, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 16 
        TCGA-QR-A70D         TCGA-WB-A814         TCGA-WB-A820 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-XG-A823         TCGA-PR-A5PG         TCGA-PR-A5PH 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-QR-A702         TCGA-QT-A5XJ         TCGA-QT-A5XP 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-RW-A680         TCGA-RW-A686         TCGA-RW-A8AZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-TT-A6YK         TCGA-WB-A80Q         TCGA-WB-A80Y 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-WB-A81W 
"16P LOSS WILD-TYPE" 
                    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
D59V9, 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(60) Variable = 16Q LOSS MUTATION ANALYSIS
D60V1, 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-QR-A700 TCGA-PR-A5PF TCGA-QT-A69Q TCGA-SR-A6MT TCGA-WB-A81S 
       32.15        17.95         0.79       106.75        23.77 

$`16Q LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        30.51        14.17         0.23       117.14        25.05 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU 
       23.90        44.52        41.88        13.87        26.96        30.51 
TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 
       18.94       121.05         3.12        19.86        17.69        74.04 
TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY 
       43.07        48.53        24.82        10.16        20.19        31.46 
TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG TCGA-PR-A5PH 
       29.03         4.04        17.75         5.88        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-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 
        9.21         9.93        14.27        31.53        15.58         1.28 
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-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
       13.12         9.01         1.41        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        47.64        37.51         1.05         0.85        19.30 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
        1.22        27.22         6.28        72.79        11.57         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        36.56        37.25        35.51        31.04 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       40.70        42.77        27.91        23.21        25.32        17.95 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       24.20         9.73       114.77       109.25        82.62        79.46 
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-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
       68.61        81.93       110.53        24.66        26.20        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        37.35        19.92        13.32        42.48        20.09 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       17.16         1.18        14.43        18.44        16.60        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       14.79        41.26        34.26         4.47         4.73        25.51 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 
      316.73       127.56        29.16        19.59        53.59        41.23 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G 
       42.35        33.90        24.16        35.84        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       63.98        22.32        24.36        40.04        45.83        62.04 
TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 
       12.99         1.61        25.51        71.05        78.21        93.11 
TCGA-WB-A822 
      103.17 

  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              25.05 
[1] "0.8 - 106.8 (23.8)" "0.1 - 316.7 (25.1)"
[1] "hr="     "2.5e+07"
D60V2, continuous
D60V3, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     5   0
  16Q LOSS WILD-TYPE 129  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5    0
  16Q LOSS WILD-TYPE  129   28
                    clus
vv                   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ADRENAL GLAND                     5                129
  EXTRA-ADRENAL SITE                0                 28
[1] 2 2
[1] FALSE
D60V4, 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
D60V5, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     5   0
  16Q LOSS WILD-TYPE 150   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5    0
  16Q LOSS WILD-TYPE  150    5
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 5                150
  YES                0                  5
[1] 2 2
[1] FALSE
D60V6, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 58 
        TCGA-S7-A7WQ         TCGA-S7-A7WU         TCGA-S7-A7X1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SR-A6MV         TCGA-WB-A817         TCGA-WB-A81E 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-XG-A823         TCGA-P7-A5NY         TCGA-PR-A5PG 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-PR-A5PH         TCGA-RT-A6YA         TCGA-RT-A6YC 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-RX-A8JQ         TCGA-S7-A7WL         TCGA-S7-A7WM 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-S7-A7WN         TCGA-S7-A7WO         TCGA-S7-A7WP 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-S7-A7WR         TCGA-S7-A7WT         TCGA-S7-A7WV 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-S7-A7WW         TCGA-S7-A7WX         TCGA-S7-A7X0 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-S7-A7X2         TCGA-SP-A6QC         TCGA-SP-A6QD 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SP-A6QF         TCGA-SP-A6QG         TCGA-SP-A6QI 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SP-A6QJ         TCGA-SP-A6QK         TCGA-SR-A6MQ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SR-A6MS         TCGA-SR-A6MY         TCGA-SR-A6MZ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-SR-A6N0         TCGA-TT-A6YK         TCGA-TT-A6YN 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-TT-A6YO         TCGA-TT-A6YP         TCGA-WB-A80K 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-WB-A80L         TCGA-WB-A80Q         TCGA-WB-A815 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-WB-A818         TCGA-WB-A81D         TCGA-WB-A81F 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-WB-A81G         TCGA-WB-A81H         TCGA-WB-A81I 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-WB-A81J         TCGA-WB-A81K         TCGA-WB-A81M 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-WB-A81N         TCGA-WB-A81T         TCGA-WB-A821 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-WB-A822 
"16Q LOSS WILD-TYPE" 
                    vv
clus                 PARAGANGLIOMA
  16Q LOSS MUTATED               0
  16Q LOSS WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  16Q LOSS MUTATED                                               0
  16Q LOSS WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  16Q LOSS MUTATED                  5
  16Q LOSS WILD-TYPE              130
D60V7, multiclass
                                               clus
vv                                              16Q LOSS MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                             5
                                               clus
vv                                              16Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V8, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 17 
        TCGA-QR-A70D         TCGA-QR-A70P         TCGA-WB-A814 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-WB-A820         TCGA-XG-A823         TCGA-PR-A5PG 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-PR-A5PH         TCGA-QR-A702         TCGA-QT-A5XJ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-QT-A5XP         TCGA-RW-A680         TCGA-RW-A686 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-RW-A8AZ         TCGA-TT-A6YK         TCGA-WB-A80Q 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-WB-A80Y         TCGA-WB-A81W 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
                    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
D60V9, 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(61) Variable = 17P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   60  2
  17P LOSS WILD-TYPE 96  4
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                62                100 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                  4 
$`17P LOSS MUTATED`
TCGA-QR-A6GU TCGA-QR-A6H1 TCGA-RW-A68A TCGA-RW-A68F TCGA-RW-A68G TCGA-S7-A7WQ 
       58.88        14.17        25.05        44.52        41.88        26.96 
TCGA-S7-A7X1 TCGA-WB-A81Q TCGA-PR-A5PG TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GY 
       18.94        24.82        81.70        23.11         1.25         1.05 
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-A5XP TCGA-QT-A69Q TCGA-RW-A67X TCGA-RW-A67Y 
        6.02        25.18         4.41         0.79         2.93         7.10 
TCGA-RW-A681 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A7D0 
       37.51         0.85         1.22        27.22         6.28        11.57 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WT TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X2 
       31.59        36.56        42.77        23.21        25.32        24.20 
TCGA-SP-A6QD TCGA-SP-A6QJ TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MT TCGA-TT-A6YJ 
      109.25        15.52         0.10        68.61       106.75         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7UY TCGA-WB-A80N 
       37.35        19.92         1.18        14.43        14.79         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A818 
       25.51       316.73        29.16        19.59        53.59        42.35 
TCGA-WB-A81J TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81S TCGA-WB-A81T 
       24.36        45.83        62.04        12.99        23.77        25.51 
TCGA-WB-A81W TCGA-WB-A822 
       78.21       103.17 

$`17P LOSS WILD-TYPE`
TCGA-QR-A6GZ TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68B TCGA-RW-A7CZ 
       30.51        32.15         0.23       117.14        23.90        13.87 
TCGA-S7-A7WU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 
       30.51       121.05         3.12        19.86        17.69        74.04 
TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       43.07        48.53        10.16        20.19        31.46        29.03 
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PH TCGA-QR-A6GO 
        4.04        17.75         5.88        17.95        28.08        35.01 
TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6H0 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
      137.59        19.04         9.21        14.27        31.53        15.58 
TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70K 
        4.11       116.19         6.31         2.33        26.83         9.01 
TCGA-QR-A70N TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
        1.41        12.39        17.95        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        0.72         2.30        13.08        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A680 TCGA-RW-A684 
       50.63         8.09        86.89        19.86        47.64         1.05 
TCGA-RW-A686 TCGA-RW-A68D TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WO 
       19.30        72.79         2.89        20.09        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WV TCGA-S7-A7X0 TCGA-SA-A6C2 TCGA-SP-A6QC 
       31.04        40.70        27.91        17.95         9.73       114.77 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP 
       82.62        79.46       110.04       111.25         1.41        51.22 
TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YO 
       81.93       110.53        24.66        26.20        49.61        13.32 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       42.48        20.09        17.16        18.44        16.60        25.61 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80Q TCGA-WB-A816 TCGA-WB-A819 
       41.26        34.26         4.47       127.56        41.23        33.90 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       24.16        35.84        57.11        38.76        63.98        22.32 
TCGA-WB-A81K TCGA-WB-A81R TCGA-WB-A81V TCGA-WB-A821 
       40.04         1.61        71.05        93.11 

  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 
            24.280             26.515 
[1] "0.1 - 316.7 (24.3)" "0.2 - 137.6 (26.5)"
[1] "hr=" "1"  
D61V2, continuous
D61V3, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   57  5
  17P LOSS WILD-TYPE 77 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     57    5
  17P LOSS WILD-TYPE   77   23
                    clus
vv                   17P LOSS MUTATED 17P LOSS WILD-TYPE
  ADRENAL GLAND                    57                 77
  EXTRA-ADRENAL SITE                5                 23
[1] 2 2
[1] FALSE
D61V4, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   31 31
  17P LOSS WILD-TYPE 57 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     31   31
  17P LOSS WILD-TYPE   57   43
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               31                 57
  MALE                 31                 43
[1] 2 2
[1] FALSE
D61V5, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   58  3
  17P LOSS WILD-TYPE 97  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     58    3
  17P LOSS WILD-TYPE   97    2
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                58                 97
  YES                3                  2
[1] 2 2
[1] FALSE
D61V6, continuous
                    vv
clus                 PARAGANGLIOMA
  17P LOSS MUTATED               3
  17P LOSS WILD-TYPE            13
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  17P LOSS MUTATED                                               2
  17P LOSS WILD-TYPE                                             9
                    vv
clus                 PHEOCHROMOCYTOMA
  17P LOSS MUTATED                 57
  17P LOSS WILD-TYPE               78
D61V7, multiclass
                                               clus
vv                                              17P LOSS MUTATED
  PARAGANGLIOMA                                                3
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                2
  PHEOCHROMOCYTOMA                                            57
                                               clus
vv                                              17P LOSS WILD-TYPE
  PARAGANGLIOMA                                                 13
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                  9
  PHEOCHROMOCYTOMA                                              78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V8, continuous
                    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                           4    53
  17P LOSS WILD-TYPE                        15    81
D61V9, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  3
  BLACK OR AFRICAN AMERICAN                       4                 15
  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(62) Variable = 17Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    14   1
  17Q LOSS WILD-TYPE 142   5
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                15                147 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                  5 
$`17Q LOSS MUTATED`
TCGA-QR-A700 TCGA-S7-A7WQ TCGA-S7-A7X1 TCGA-WB-A820 TCGA-QR-A70J TCGA-QT-A5XP 
       32.15        26.96        18.94        10.16        13.12         4.41 
TCGA-QT-A69Q TCGA-RT-A6YA TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A688 TCGA-RW-A68C 
        0.79        50.63         2.93         7.10         1.22         6.28 
TCGA-SQ-A6I6 TCGA-SR-A6MT TCGA-WB-A81N 
        0.10       106.75        62.04 

$`17Q LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        30.51        14.17         0.23       117.14        25.05 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WU TCGA-SR-A6MV 
       23.90        44.52        41.88        13.87        30.51       121.05 
TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E 
        3.12        19.86        17.69        74.04        43.07        48.53 
TCGA-WB-A81Q TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX 
       24.82        20.19        31.46        29.03         4.04        17.75 
TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR 
        5.88        17.95        81.70        28.08        35.01        23.11 
TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 
        1.25       137.59        19.04         1.05         9.21         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-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70K TCGA-QR-A70N 
        6.31         2.33        26.83        29.92         9.01         1.41 
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-A7U0 
        6.94         1.81         0.72        25.18         2.30        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
       77.98         0.92       108.26         8.09        86.89        19.86 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A689 
       47.64        37.51         1.05         0.85        19.30        27.22 
TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
       72.79        11.57         2.89        20.09        31.59        36.56 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV 
       37.25        35.51        31.04        40.70        42.77        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       23.21        25.32        17.95        24.20         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        79.46       110.04        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MY 
        1.41        51.22        68.61        81.93       110.53        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       26.20        49.61         4.34        37.35        19.92        13.32 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD 
       42.48        20.09        17.16         1.18        14.43        18.44 
TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       16.60        25.61        14.79        41.26        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73        25.51       316.73       127.56        29.16        19.59 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
       53.59        41.23        42.35        33.90        24.16        35.84 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       57.11        38.76        63.98        22.32        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       45.83        12.99         1.61        23.77        25.51        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       78.21        93.11       103.17 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.10               0.23 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            106.75             316.73 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             10.16              25.32 
[1] "0.1 - 106.8 (10.2)" "0.2 - 316.7 (25.3)"
[1] "hr=" "3.5"
D62V2, continuous
D62V3, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    15   0
  17Q LOSS WILD-TYPE 119  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     15    0
  17Q LOSS WILD-TYPE  119   28
                    clus
vv                   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ADRENAL GLAND                    15                119
  EXTRA-ADRENAL SITE                0                 28
[1] 2 2
[1] FALSE
D62V4, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    7  8
  17Q LOSS WILD-TYPE 81 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      7    8
  17Q LOSS WILD-TYPE   81   66
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                7                 81
  MALE                  8                 66
[1] 2 2
[1] FALSE
D62V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    14   0
  17Q LOSS WILD-TYPE 141   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     14    0
  17Q LOSS WILD-TYPE  141    5
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                14                141
  YES                0                  5
[1] 2 2
[1] FALSE
D62V6, continuous
                    vv
clus                 PARAGANGLIOMA
  17Q LOSS MUTATED               0
  17Q LOSS WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  17Q LOSS MUTATED                                               0
  17Q LOSS WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  17Q LOSS MUTATED                 15
  17Q LOSS WILD-TYPE              120
D62V7, multiclass
                                               clus
vv                                              17Q LOSS MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                            15
                                               clus
vv                                              17Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V8, continuous
                    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    14
  17Q LOSS WILD-TYPE                        18   120
D62V9, 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                                          14                120
[1] 4 2
[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 = 18P LOSS MUTATION ANALYSIS
D63V1, 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-RW-A68G TCGA-P8-A5KD TCGA-QR-A6GY TCGA-QR-A6H2 TCGA-QR-A6H6 TCGA-QR-A70C 
       41.88         4.04         1.05         9.93        15.58       116.19 
TCGA-QR-A70I TCGA-QR-A7IP TCGA-RW-A67X TCGA-S7-A7X2 TCGA-SP-A6QF TCGA-W2-A7H7 
       29.92        17.95         2.93        24.20        82.62        17.16 
TCGA-WB-A80O TCGA-WB-A819 TCGA-WB-A81W TCGA-WB-A821 
       25.51        33.90        78.21        93.11 

$`18P LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU 
       25.05        23.90        44.52        13.87        26.96        30.51 
TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 
       18.94       121.05         3.12        19.86        17.69        74.04 
TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY 
       43.07        48.53        24.82        10.16        20.19        31.46 
TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH 
       29.03        17.75         5.88        17.95        81.70        28.08 
TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6H0 
       35.01        23.11         1.25       137.59        19.04         9.21 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70E TCGA-QR-A70G 
       14.27        31.53         1.28         4.11         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W 
       26.83        13.12         9.01         1.41        14.20        41.79 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
        6.02        12.39        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-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        7.10        47.64        37.51         1.05         0.85        19.30 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
        1.22        27.22         6.28        72.79        11.57         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        36.56        37.25        35.51        31.04 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       40.70        42.77        27.91        23.21        25.32        17.95 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
        9.73       114.77       109.25        79.46       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-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      106.75       110.53        24.66        26.20        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HA 
       37.35        19.92        13.32        42.48        20.09         1.18 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       14.43        18.44        16.60        25.61        14.79        41.26 
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-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D 
       19.59        53.59        41.23        42.35        24.16        35.84 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       57.11        38.76        63.98        22.32        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       45.83        62.04        12.99         1.61        23.77        25.51 
TCGA-WB-A81V TCGA-WB-A822 
       71.05       103.17 

  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 
            24.855             24.935 
[1] "1.1 - 116.2 (24.9)" "0.1 - 316.7 (24.9)"
[1] "hr="     "7.7e+07"
D63V2, continuous
D63V3, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    13   3
  18P LOSS WILD-TYPE 121  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     13    3
  18P LOSS WILD-TYPE  121   25
                    clus
vv                   18P LOSS MUTATED 18P LOSS WILD-TYPE
  ADRENAL GLAND                    13                121
  EXTRA-ADRENAL SITE                3                 25
[1] 2 2
[1] FALSE
D63V4, 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
D63V5, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    16   0
  18P LOSS WILD-TYPE 139   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     16    0
  18P LOSS WILD-TYPE  139    5
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                16                139
  YES                0                  5
[1] 2 2
[1] FALSE
D63V6, continuous
                    vv
clus                 PARAGANGLIOMA
  18P LOSS MUTATED               3
  18P LOSS WILD-TYPE            13
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  18P LOSS MUTATED                                               0
  18P LOSS WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  18P LOSS MUTATED                 13
  18P LOSS WILD-TYPE              122
D63V7, multiclass
                                               clus
vv                                              18P LOSS MUTATED
  PARAGANGLIOMA                                                3
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                            13
                                               clus
vv                                              18P LOSS WILD-TYPE
  PARAGANGLIOMA                                                 13
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V8, continuous
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                 17 
        TCGA-QR-A70D         TCGA-QR-A70P         TCGA-WB-A814 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-WB-A820         TCGA-XG-A823         TCGA-PR-A5PG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-PR-A5PH         TCGA-QR-A702         TCGA-QT-A5XJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-QT-A5XP         TCGA-QT-A69Q         TCGA-RW-A680 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-RW-A686         TCGA-RW-A8AZ         TCGA-TT-A6YK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-WB-A80Q         TCGA-WB-A80Y 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
                    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
D63V9, 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(64) Variable = 18Q LOSS MUTATION ANALYSIS
D64V1, 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-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 
       74.04        43.07        48.53        24.82        10.16        20.19 
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         4.04        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-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A702 
       19.04         1.05         9.21        14.27        31.53         1.28 
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-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A70X 
       13.12         9.01         1.41        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 
       47.64        37.51         1.05         0.85        19.30         1.22 
TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       27.22         6.28        72.79        11.57         2.89        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR 
       31.59        36.56        37.25        35.51        31.04        40.70 
TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 
       42.77        27.91        23.21        25.32        17.95        24.20 
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        79.46       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-A6MT TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
       81.93       106.75       110.53        24.66        26.20        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        37.35        19.92        13.32        42.48        20.09 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       17.16         1.18        14.43        18.44        16.60        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       14.79        41.26        34.26         4.47         4.73        25.51 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 
      316.73       127.56        29.16        19.59        53.59        41.23 
TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       42.35        24.16        35.84        57.11        38.76        63.98 
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        62.04        12.99 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 
        1.61        23.77        25.51        71.05        78.21       103.17 

  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             25.115 
[1] "2.3 - 93.1 (16.8)"  "0.1 - 316.7 (25.1)"
[1] "hr="     "2.5e+07"
D64V2, continuous
D64V3, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     4   2
  18Q LOSS WILD-TYPE 130  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4    2
  18Q LOSS WILD-TYPE  130   26
                    clus
vv                   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ADRENAL GLAND                     4                130
  EXTRA-ADRENAL SITE                2                 26
[1] 2 2
[1] FALSE
D64V4, 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
D64V5, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     6   0
  18Q LOSS WILD-TYPE 149   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      6    0
  18Q LOSS WILD-TYPE  149    5
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 6                149
  YES                0                  5
[1] 2 2
[1] FALSE
D64V6, continuous
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 1                 59 
        TCGA-S7-A7WQ         TCGA-S7-A7WU         TCGA-S7-A7X1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-SR-A6MV         TCGA-WB-A817         TCGA-WB-A81E 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-XG-A823         TCGA-P7-A5NY         TCGA-PR-A5PF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-PR-A5PG         TCGA-PR-A5PH         TCGA-RT-A6YA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-RT-A6YC         TCGA-RX-A8JQ         TCGA-S7-A7WL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-S7-A7WM         TCGA-S7-A7WN         TCGA-S7-A7WO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-S7-A7WP         TCGA-S7-A7WR         TCGA-S7-A7WT 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-S7-A7WV         TCGA-S7-A7WW         TCGA-S7-A7WX 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-S7-A7X0         TCGA-S7-A7X2         TCGA-SP-A6QC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-SP-A6QD         TCGA-SP-A6QF         TCGA-SP-A6QG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-SP-A6QI         TCGA-SP-A6QJ         TCGA-SP-A6QK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-SR-A6MQ         TCGA-SR-A6MS         TCGA-SR-A6MY 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-SR-A6MZ         TCGA-SR-A6N0         TCGA-TT-A6YK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-TT-A6YN         TCGA-TT-A6YO         TCGA-TT-A6YP 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-WB-A80K         TCGA-WB-A80L         TCGA-WB-A80Q 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-WB-A815         TCGA-WB-A818         TCGA-WB-A81D 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-WB-A81F         TCGA-WB-A81G         TCGA-WB-A81H 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-WB-A81I         TCGA-WB-A81J         TCGA-WB-A81K 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-WB-A81M         TCGA-WB-A81N         TCGA-WB-A81S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-WB-A81T         TCGA-WB-A822 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
                    vv
clus                 PARAGANGLIOMA
  18Q LOSS MUTATED               2
  18Q LOSS WILD-TYPE            14
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  18Q LOSS MUTATED                                               0
  18Q LOSS WILD-TYPE                                            11
                    vv
clus                 PHEOCHROMOCYTOMA
  18Q LOSS MUTATED                  4
  18Q LOSS WILD-TYPE              131
D64V7, multiclass
                                               clus
vv                                              18Q LOSS MUTATED
  PARAGANGLIOMA                                                2
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                0
  PHEOCHROMOCYTOMA                                             4
                                               clus
vv                                              18Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                 14
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 11
  PHEOCHROMOCYTOMA                                             131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V8, continuous
                    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
D64V9, 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(65) Variable = 19Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED     5   0
  19Q LOSS WILD-TYPE 151   6
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 5                157 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 0                  6 
$`19Q LOSS MUTATED`
TCGA-QR-A70R TCGA-SP-A6QG TCGA-SR-A6MQ TCGA-TT-A6YK TCGA-WB-A81S 
       14.20        79.46        68.61        37.35        23.77 

$`19Q LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 
       74.04        43.07        48.53        24.82        10.16        20.19 
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         4.04        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-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
       19.04         1.05         9.21         9.93        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G 
       15.58         1.28         4.11       116.19         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70W 
       26.83        29.92        13.12         9.01         1.41        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        47.64        37.51         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D 
        0.85        19.30         1.22        27.22         6.28        72.79 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
       11.57         2.89        20.09        31.59        36.56        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW 
       35.51        31.04        40.70        42.77        27.91        23.21 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       25.32        17.95        24.20         9.73       114.77       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-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ 
       51.22        81.93       106.75       110.53        24.66        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
       49.61         4.34        19.92        13.32        42.48        20.09 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       17.16         1.18        14.43        18.44        16.60        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       14.79        41.26        34.26         4.47         4.73        25.51 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 
      316.73       127.56        29.16        19.59        53.59        41.23 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G 
       42.35        33.90        24.16        35.84        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       63.98        22.32        24.36        40.04        45.83        62.04 
TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 
       12.99         1.61        25.51        71.05        78.21        93.11 
TCGA-WB-A822 
      103.17 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              14.2                0.1 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             79.46             316.73 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             37.35              24.82 
[1] "14.2 - 79.5 (37.4)" "0.1 - 316.7 (24.8)"
[1] "hr="     "2.6e+07"
D65V2, continuous
D65V3, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     2   3
  19Q LOSS WILD-TYPE 132  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    3
  19Q LOSS WILD-TYPE  132   25
                    clus
vv                   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ADRENAL GLAND                     2                132
  EXTRA-ADRENAL SITE                3                 25
[1] 2 2
[1] FALSE
D65V4, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    3  2
  19Q LOSS WILD-TYPE 85 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3    2
  19Q LOSS WILD-TYPE   85   72
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                3                 85
  MALE                  2                 72
[1] 2 2
[1] FALSE
D65V5, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     5   0
  19Q LOSS WILD-TYPE 150   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      5    0
  19Q LOSS WILD-TYPE  150    5
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 5                150
  YES                0                  5
[1] 2 2
[1] FALSE
D65V6, continuous
                    vv
clus                 PARAGANGLIOMA
  19Q LOSS MUTATED               2
  19Q LOSS WILD-TYPE            14
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  19Q LOSS MUTATED                                               1
  19Q LOSS WILD-TYPE                                            10
                    vv
clus                 PHEOCHROMOCYTOMA
  19Q LOSS MUTATED                  2
  19Q LOSS WILD-TYPE              133
D65V7, multiclass
                                               clus
vv                                              19Q LOSS MUTATED
  PARAGANGLIOMA                                                2
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                1
  PHEOCHROMOCYTOMA                                             2
                                               clus
vv                                              19Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                 14
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 10
  PHEOCHROMOCYTOMA                                             133
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V8, continuous
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                 17 
        TCGA-QR-A70D         TCGA-QR-A70P         TCGA-WB-A814 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-WB-A820         TCGA-XG-A823         TCGA-PR-A5PG 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-PR-A5PH         TCGA-QR-A702         TCGA-QT-A5XJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-QT-A5XP         TCGA-QT-A69Q         TCGA-RW-A680 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-RW-A686         TCGA-RW-A8AZ         TCGA-WB-A80Q 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-WB-A80Y         TCGA-WB-A81W 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
                    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     4
  19Q LOSS WILD-TYPE                        19   130
D65V9, 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                                           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(66) Variable = 20Q LOSS MUTATION ANALYSIS
D66V1, 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        14.43        14.79 

$`20Q LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ 
       25.05        23.90        44.52        41.88        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       30.51        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 
       74.04        43.07        48.53        24.82        10.16        20.19 
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       31.46        29.03         4.04        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-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
       19.04         1.05         9.21         9.93        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G 
       15.58         1.28         4.11       116.19         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R 
       26.83        29.92        13.12         9.01         1.41        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        47.64        37.51         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D 
        0.85        19.30         1.22        27.22         6.28        72.79 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
       11.57         2.89        20.09        31.59        36.56        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW 
       35.51        31.04        40.70        42.77        27.91        23.21 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       25.32        17.95        24.20         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        79.46       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-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        26.20        49.61         4.34        37.35        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HD 
       13.32        42.48        20.09        17.16         1.18        18.44 
TCGA-W2-A7HE TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       16.60        25.61        41.26        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 
       25.51       316.73       127.56        29.16        19.59        53.59 
TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F 
       41.23        42.35        33.90        24.16        35.84        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        63.98        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       62.04        12.99         1.61        23.77        25.51        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       78.21        93.11       103.17 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              0.92               0.10 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             14.79             316.73 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             14.43              25.18 
[1] "0.9 - 14.8 (14.4)"  "0.1 - 316.7 (25.2)"
[1] "hr="     "3300000"
D66V2, continuous
D66V3, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     2   1
  20Q LOSS WILD-TYPE 132  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    1
  20Q LOSS WILD-TYPE  132   27
                    clus
vv                   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ADRENAL GLAND                     2                132
  EXTRA-ADRENAL SITE                1                 27
[1] 2 2
[1] FALSE
D66V4, 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
D66V5, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     3   0
  20Q LOSS WILD-TYPE 152   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    0
  20Q LOSS WILD-TYPE  152    5
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 3                152
  YES                0                  5
[1] 2 2
[1] FALSE
D66V6, continuous
                    vv
clus                 PARAGANGLIOMA
  20Q LOSS MUTATED               0
  20Q LOSS WILD-TYPE            16
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  20Q LOSS MUTATED                                               1
  20Q LOSS WILD-TYPE                                            10
                    vv
clus                 PHEOCHROMOCYTOMA
  20Q LOSS MUTATED                  2
  20Q LOSS WILD-TYPE              133
D66V7, multiclass
                                               clus
vv                                              20Q LOSS MUTATED
  PARAGANGLIOMA                                                0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                1
  PHEOCHROMOCYTOMA                                             2
                                               clus
vv                                              20Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                 16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 10
  PHEOCHROMOCYTOMA                                             133
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V8, continuous
                    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
D66V9, 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(67) Variable = 21Q LOSS MUTATION ANALYSIS
D67V1, 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-QR-A700 TCGA-S7-A7WQ TCGA-SR-A6MV TCGA-W2-A7HB TCGA-PR-A5PF TCGA-QR-A6GO 
       32.15        26.96       121.05        19.86        17.95        35.01 
TCGA-QR-A6H2 TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QT-A5XK TCGA-QT-A5XM 
        9.93         9.01         1.41        14.20         6.94         0.72 
TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RW-A67W TCGA-RW-A684 TCGA-RW-A68C TCGA-S7-A7WP 
        2.30         0.79        19.86         1.05         6.28        31.04 
TCGA-SP-A6QC TCGA-SP-A6QK TCGA-SR-A6MP TCGA-SR-A6MT TCGA-SR-A6MZ TCGA-TT-A6YK 
      114.77       111.25        51.22       106.75        26.20        37.35 
TCGA-TT-A6YN TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-WB-A80L TCGA-WB-A815 
       19.92        20.09        17.16         1.18        34.26        53.59 
TCGA-WB-A816 TCGA-WB-A819 TCGA-WB-A81H TCGA-WB-A81M TCGA-WB-A81S TCGA-WB-A821 
       41.23        33.90        63.98        45.83        23.77        93.11 

$`21Q LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A 
       58.88        30.51        14.17         0.23       117.14        25.05 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WU TCGA-S7-A7X1 
       23.90        44.52        41.88        13.87        30.51        18.94 
TCGA-SR-A6MX TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q 
        3.12        17.69        74.04        43.07        48.53        24.82 
TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX 
       10.16        20.19        31.46        29.03         4.04        17.75 
TCGA-P8-A6RY TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
        5.88        81.70        28.08        23.11         1.25       137.59 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 
       19.04         1.05         9.21        14.27        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.28         4.11       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
       29.92        13.12        41.79         6.02        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T 
       36.23         1.81        25.18         4.41        13.08        77.98 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67X 
        0.92       108.26        50.63         8.09        86.89         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
        7.10        47.64        37.51         0.85        19.30         1.22 
TCGA-RW-A689 TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
       27.22        72.79        11.57         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV 
       36.56        37.25        35.51        40.70        42.77        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QD 
       23.21        25.32        17.95        24.20         9.73       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       82.62        79.46       110.04        15.52         1.41         0.10 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6N0 TCGA-TT-A6YJ 
       68.61        81.93       110.53        24.66        49.61         4.34 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       13.32        42.48        14.43        18.44        16.60        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       14.79        41.26         4.47         4.73        25.51       316.73 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D 
      127.56        29.16        19.59        42.35        24.16        35.84 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81N 
       57.11        38.76        22.32        24.36        40.04        62.04 
TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 
       12.99         1.61        25.51        71.05        78.21       103.17 

  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 
            24.985             24.935 
[1] "0.7 - 121.0 (25.0)" "0.1 - 316.7 (24.9)"
[1] "hr="     "2.6e+08"
D67V2, continuous
D67V3, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    34   2
  21Q LOSS WILD-TYPE 100  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     34    2
  21Q LOSS WILD-TYPE  100   26
                    clus
vv                   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ADRENAL GLAND                    34                100
  EXTRA-ADRENAL SITE                2                 26
[1] 2 2
[1] FALSE
D67V4, 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
D67V5, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    35   1
  21Q LOSS WILD-TYPE 120   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     35    1
  21Q LOSS WILD-TYPE  120    4
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                35                120
  YES                1                  4
[1] 2 2
[1] FALSE
D67V6, continuous
                    vv
clus                 PARAGANGLIOMA
  21Q LOSS MUTATED               1
  21Q LOSS WILD-TYPE            15
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  21Q LOSS MUTATED                                               1
  21Q LOSS WILD-TYPE                                            10
                    vv
clus                 PHEOCHROMOCYTOMA
  21Q LOSS MUTATED                 34
  21Q LOSS WILD-TYPE              101
D67V7, multiclass
                                               clus
vv                                              21Q LOSS MUTATED
  PARAGANGLIOMA                                                1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                1
  PHEOCHROMOCYTOMA                                            34
                                               clus
vv                                              21Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                 15
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 10
  PHEOCHROMOCYTOMA                                             101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V8, continuous
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                 16 
        TCGA-QR-A70D         TCGA-QR-A70P         TCGA-WB-A814 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-WB-A820         TCGA-XG-A823         TCGA-PR-A5PG 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-PR-A5PH         TCGA-QR-A702         TCGA-QT-A5XJ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-QT-A5XP         TCGA-RW-A680         TCGA-RW-A686 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-RW-A8AZ         TCGA-WB-A80Q         TCGA-WB-A80Y 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-WB-A81W 
"21Q LOSS WILD-TYPE" 
                    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
D67V9, 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(68) Variable = 22Q LOSS MUTATION ANALYSIS
D68V1, 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-QR-A70P TCGA-S7-A7WQ TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A81Q 
      117.14        26.96         3.12        19.86        17.69        24.82 
TCGA-WB-A820 TCGA-XG-A823 TCGA-P8-A5KD TCGA-P8-A6RY TCGA-PR-A5PF TCGA-QR-A6GR 
       10.16        20.19         4.04         5.88        17.95        23.11 
TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
       15.58         1.28       116.19         6.31         2.33        26.83 
TCGA-QR-A70K TCGA-QR-A70W TCGA-QT-A5XK TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q 
        9.01        41.79         6.94         2.30         4.41         0.79 
TCGA-RT-A6Y9 TCGA-RW-A67Y TCGA-RW-A681 TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WR 
      108.26         7.10        37.51        31.59        36.56        40.70 
TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QJ TCGA-SP-A6QK 
       25.32        24.20        82.62        79.46        15.52       111.25 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MZ TCGA-TT-A6YK TCGA-W2-A7H5 TCGA-W2-A7HA 
        0.10        51.22        26.20        37.35        20.09         1.18 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7UY TCGA-WB-A80N TCGA-WB-A80O 
       14.43        18.44        16.60        14.79         4.73        25.51 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81H 
       29.16        19.59        53.59        33.90        24.16        63.98 
TCGA-WB-A81N TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81W 
       62.04         1.61        25.51        78.21 

$`22Q LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-RW-A68A 
       58.88        30.51        14.17        32.15         0.23        25.05 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WU TCGA-S7-A7X1 
       23.90        44.52        41.88        13.87        30.51        18.94 
TCGA-SR-A6MV TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-P7-A5NY TCGA-P8-A5KC 
      121.05        74.04        43.07        48.53        31.46        29.03 
TCGA-P8-A6RX TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GS TCGA-QR-A6GT 
       17.75        81.70        28.08        35.01         1.25       137.59 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
       19.04         1.05         9.21         9.93        14.27        31.53 
TCGA-QR-A706 TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70X 
        4.11        29.92        13.12         1.41        14.20         6.02 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
       12.39        17.95        36.23         1.81         0.72        25.18 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       13.08        77.98         0.92        50.63         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
       19.86         2.93        47.64         1.05         0.85        19.30 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
        1.22        27.22         6.28        72.79        11.57         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WT TCGA-S7-A7WV 
       20.09        37.25        35.51        31.04        42.77        27.91 
TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QI 
       23.21        17.95         9.73       114.77       109.25       110.04 
TCGA-SQ-A6I4 TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MY 
        1.41        68.61        81.93       106.75       110.53        24.66 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 
       49.61         4.34        19.92        13.32        42.48        17.16 
TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80P TCGA-WB-A80Q 
       25.61        41.26        34.26         4.47       316.73       127.56 
TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81I 
       41.23        42.35        35.84        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 
            21.650             27.565 
[1] "0.1 - 117.1 (21.6)" "0.2 - 316.7 (27.6)"
[1] "hr=" "11" 
D68V2, continuous
D68V3, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   52  6
  22Q LOSS WILD-TYPE 82 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     52    6
  22Q LOSS WILD-TYPE   82   22
                    clus
vv                   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ADRENAL GLAND                    52                 82
  EXTRA-ADRENAL SITE                6                 22
[1] 2 2
[1] FALSE
D68V4, 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
D68V5, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    55   2
  22Q LOSS WILD-TYPE 100   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     55    2
  22Q LOSS WILD-TYPE  100    3
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                55                100
  YES                2                  3
[1] 2 2
[1] FALSE
D68V6, continuous
                    vv
clus                 PARAGANGLIOMA
  22Q LOSS MUTATED               5
  22Q LOSS WILD-TYPE            11
                    vv
clus                 PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  22Q LOSS MUTATED                                               1
  22Q LOSS WILD-TYPE                                            10
                    vv
clus                 PHEOCHROMOCYTOMA
  22Q LOSS MUTATED                 52
  22Q LOSS WILD-TYPE               83
D68V7, multiclass
                                               clus
vv                                              22Q LOSS MUTATED
  PARAGANGLIOMA                                                5
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                1
  PHEOCHROMOCYTOMA                                            52
                                               clus
vv                                              22Q LOSS WILD-TYPE
  PARAGANGLIOMA                                                 11
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                 10
  PHEOCHROMOCYTOMA                                              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V8, continuous
                    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
D68V9, 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(69) Variable = XP LOSS MUTATION ANALYSIS
D69V1, 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-RW-A68A TCGA-S7-A7WQ TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       25.05        26.96       121.05         3.12        19.86        17.69 
TCGA-WB-A81E TCGA-WB-A820 TCGA-QR-A6GO TCGA-QR-A6GT TCGA-QR-A6H6 TCGA-QR-A702 
       48.53        10.16        35.01       137.59        15.58         1.28 
TCGA-QR-A70H TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A7IN TCGA-QR-A7IP 
       26.83         9.01        14.20        41.79        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RT-A6YA 
       36.23         6.94        25.18         2.30         0.79        50.63 
TCGA-RW-A67Y TCGA-RW-A689 TCGA-RW-A68C TCGA-S7-A7WR TCGA-S7-A7WX TCGA-SP-A6QG 
        7.10        27.22         6.28        40.70        25.32        79.46 
TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-W2-A7H7 
        0.10        68.61        24.66         4.34        19.92        17.16 
TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7UY TCGA-WB-A80M TCGA-WB-A80V 
        1.18        14.43        18.44        14.79         4.47        29.16 
TCGA-WB-A815 TCGA-WB-A819 TCGA-WB-A81F TCGA-WB-A81K TCGA-WB-A81R TCGA-WB-A81W 
       53.59        33.90        57.11        40.04         1.61        78.21 

$`XP LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WU TCGA-S7-A7X1 
       23.90        44.52        41.88        13.87        30.51        18.94 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81Q TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       74.04        43.07        24.82        20.19        31.46        29.03 
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH 
        4.04        17.75         5.88        17.95        81.70        28.08 
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 
       23.11         1.25        19.04         1.05         9.21         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G 
       14.27        31.53         4.11       116.19         6.31         2.33 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70X TCGA-QT-A5XL TCGA-QT-A5XM 
       29.92        13.12         1.41         6.02         1.81         0.72 
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-A67X TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       86.89        19.86         2.93        47.64        37.51         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
        0.85        19.30         1.22        72.79        11.57         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        36.56        37.25        35.51        31.04 
TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 
       42.77        27.91        23.21        17.95        24.20         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-SR-A6MP TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MZ 
        1.41        51.22        81.93       106.75       110.53        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HE 
       49.61        37.35        13.32        42.48        20.09        16.60 
TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       25.61        41.26        34.26         4.73        25.51       316.73 
TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D 
      127.56        19.59        41.23        42.35        24.16        35.84 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81M TCGA-WB-A81N 
       38.76        63.98        22.32        24.36        45.83        62.04 
TCGA-WB-A81P TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A821 TCGA-WB-A822 
       12.99        23.77        25.51        71.05        93.11       103.17 

  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 
            19.89             25.56 
[1] "0.1 - 137.6 (19.9)" "0.2 - 316.7 (25.6)"
[1] "hr=" "1.2"
D69V2, continuous
D69V3, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   39  9
  XP LOSS WILD-TYPE 95 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     39    9
  XP LOSS WILD-TYPE   95   19
                    clus
vv                   XP LOSS MUTATED XP LOSS WILD-TYPE
  ADRENAL GLAND                   39                95
  EXTRA-ADRENAL SITE               9                19
[1] 2 2
[1] FALSE
D69V4, 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
D69V5, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    46   1
  XP LOSS WILD-TYPE 109   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     46    1
  XP LOSS WILD-TYPE  109    4
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               46               109
  YES               1                 4
[1] 2 2
[1] FALSE
D69V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  XP LOSS MUTATED               7                                             1
  XP LOSS WILD-TYPE             9                                            10
                   vv
clus                PHEOCHROMOCYTOMA
  XP LOSS MUTATED                 40
  XP LOSS WILD-TYPE               95
D69V7, multiclass
                                               clus
vv                                              XP LOSS MUTATED
  PARAGANGLIOMA                                               7
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               1
  PHEOCHROMOCYTOMA                                           40
                                               clus
vv                                              XP LOSS WILD-TYPE
  PARAGANGLIOMA                                                 9
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                10
  PHEOCHROMOCYTOMA                                             95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V8, continuous
                   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
D69V9, 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(70) Variable = XQ LOSS MUTATION ANALYSIS
D70V1, 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-RW-A68A TCGA-S7-A7WQ TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       25.05        26.96       121.05         3.12        19.86        17.69 
TCGA-WB-A81E TCGA-WB-A820 TCGA-QR-A6GO TCGA-QR-A6GT TCGA-QR-A6H6 TCGA-QR-A702 
       48.53        10.16        35.01       137.59        15.58         1.28 
TCGA-QR-A70H TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A7IN TCGA-QR-A7IP 
       26.83         9.01        14.20        41.79        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RT-A6YA 
       36.23         6.94        25.18         2.30         0.79        50.63 
TCGA-RW-A67Y TCGA-RW-A689 TCGA-RW-A68C TCGA-S7-A7WR TCGA-S7-A7WX TCGA-SP-A6QG 
        7.10        27.22         6.28        40.70        25.32        79.46 
TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-W2-A7H7 
        0.10        68.61        24.66         4.34        19.92        17.16 
TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7UY TCGA-WB-A80M TCGA-WB-A80V 
        1.18        14.43        18.44        14.79         4.47        29.16 
TCGA-WB-A815 TCGA-WB-A819 TCGA-WB-A81F TCGA-WB-A81K TCGA-WB-A81R TCGA-WB-A81S 
       53.59        33.90        57.11        40.04         1.61        23.77 
TCGA-WB-A81W 
       78.21 

$`XQ LOSS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-QR-A70D TCGA-QR-A70P 
       58.88        30.51        14.17        32.15         0.23       117.14 
TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WU TCGA-S7-A7X1 
       23.90        44.52        41.88        13.87        30.51        18.94 
TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81Q TCGA-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       74.04        43.07        24.82        20.19        31.46        29.03 
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH 
        4.04        17.75         5.88        17.95        81.70        28.08 
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 
       23.11         1.25        19.04         1.05         9.21         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G 
       14.27        31.53         4.11       116.19         6.31         2.33 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70X TCGA-QT-A5XL TCGA-QT-A5XM 
       29.92        13.12         1.41         6.02         1.81         0.72 
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-A67X TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       86.89        19.86         2.93        47.64        37.51         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
        0.85        19.30         1.22        72.79        11.57         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        36.56        37.25        35.51        31.04 
TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 
       42.77        27.91        23.21        17.95        24.20         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-SR-A6MP TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MZ 
        1.41        51.22        81.93       106.75       110.53        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HE 
       49.61        37.35        13.32        42.48        20.09        16.60 
TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       25.61        41.26        34.26         4.73        25.51       316.73 
TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D 
      127.56        19.59        41.23        42.35        24.16        35.84 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81M TCGA-WB-A81N 
       38.76        63.98        22.32        24.36        45.83        62.04 
TCGA-WB-A81P TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A821 TCGA-WB-A822 
       12.99        25.51        71.05        93.11       103.17 

  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 
            19.92             25.61 
[1] "0.1 - 137.6 (19.9)" "0.2 - 316.7 (25.6)"
[1] "hr=" "1.1"
D70V2, continuous
D70V3, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   40  9
  XQ LOSS WILD-TYPE 94 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     40    9
  XQ LOSS WILD-TYPE   94   19
                    clus
vv                   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ADRENAL GLAND                   40                94
  EXTRA-ADRENAL SITE               9                19
[1] 2 2
[1] FALSE
D70V4, 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
D70V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    47   1
  XQ LOSS WILD-TYPE 108   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     47    1
  XQ LOSS WILD-TYPE  108    4
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               47               108
  YES               1                 4
[1] 2 2
[1] FALSE
D70V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  XQ LOSS MUTATED               7                                             1
  XQ LOSS WILD-TYPE             9                                            10
                   vv
clus                PHEOCHROMOCYTOMA
  XQ LOSS MUTATED                 41
  XQ LOSS WILD-TYPE               94
D70V7, multiclass
                                               clus
vv                                              XQ LOSS MUTATED
  PARAGANGLIOMA                                               7
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               1
  PHEOCHROMOCYTOMA                                           41
                                               clus
vv                                              XQ LOSS WILD-TYPE
  PARAGANGLIOMA                                                 9
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                10
  PHEOCHROMOCYTOMA                                             94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V8, continuous
                   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
D70V9, 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"
