[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/22533877/transformed.cor.cli.txt"

nPatients in clinical file=179, in cluster file=162, common to both=162
[1]  28 162
[1] "AMP PEAK 1(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                          30                          132 
  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                          30                          132 
[1] "AMP PEAK 2(4Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(4Q31.1) MUTATED AMP PEAK 2(4Q31.1) WILD-TYPE 
                          15                          147 
  AMP PEAK 2(4Q31.1) MUTATED AMP PEAK 2(4Q31.1) WILD-TYPE 
                          15                          147 
[1] "AMP PEAK 3(11P15.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 3(11P15.2) MUTATED AMP PEAK 3(11P15.2) WILD-TYPE 
                            8                           154 
  AMP PEAK 3(11P15.2) MUTATED AMP PEAK 3(11P15.2) WILD-TYPE 
                            8                           154 
[1] "AMP PEAK 4(12Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 4(12Q13.3) MUTATED AMP PEAK 4(12Q13.3) WILD-TYPE 
                           16                           146 
  AMP PEAK 4(12Q13.3) MUTATED AMP PEAK 4(12Q13.3) WILD-TYPE 
                           16                           146 
[1] "AMP PEAK 5(14Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 5(14Q24.3) MUTATED AMP PEAK 5(14Q24.3) WILD-TYPE 
                           10                           152 
  AMP PEAK 5(14Q24.3) MUTATED AMP PEAK 5(14Q24.3) WILD-TYPE 
                           10                           152 
[1] "AMP PEAK 6(17Q21.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 6(17Q21.31) MUTATED AMP PEAK 6(17Q21.31) WILD-TYPE 
                            16                            146 
  AMP PEAK 6(17Q21.31) MUTATED AMP PEAK 6(17Q21.31) WILD-TYPE 
                            16                            146 
[1] "DEL PEAK  1(1P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                        113                          49 
  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                        113                          49 
[1] "DEL PEAK  2(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                         21                         141 
  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                         21                         141 
[1] "DEL PEAK  3(3P24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                           64                            98 
  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                           64                            98 
[1] "DEL PEAK  4(3Q26.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                           93                            69 
  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                           93                            69 
[1] "DEL PEAK  5(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(4Q22.1) MUTATED DEL PEAK  5(4Q22.1) WILD-TYPE 
                           13                           149 
  DEL PEAK  5(4Q22.1) MUTATED DEL PEAK  5(4Q22.1) WILD-TYPE 
                           13                           149 
[1] "DEL PEAK  6(4Q34.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q34.2) MUTATED DEL PEAK  6(4Q34.2) WILD-TYPE 
                           13                           149 
  DEL PEAK  6(4Q34.2) MUTATED DEL PEAK  6(4Q34.2) WILD-TYPE 
                           13                           149 
[1] "DEL PEAK  7(5Q15) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(5Q15) MUTATED DEL PEAK  7(5Q15) WILD-TYPE 
                         12                         150 
  DEL PEAK  7(5Q15) MUTATED DEL PEAK  7(5Q15) WILD-TYPE 
                         12                         150 
[1] "DEL PEAK  8(6P12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(6P12.3) MUTATED DEL PEAK  8(6P12.3) WILD-TYPE 
                           10                           152 
  DEL PEAK  8(6P12.3) MUTATED DEL PEAK  8(6P12.3) WILD-TYPE 
                           10                           152 
[1] "DEL PEAK  9(6Q16.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(6Q16.1) MUTATED DEL PEAK  9(6Q16.1) WILD-TYPE 
                           24                           138 
  DEL PEAK  9(6Q16.1) MUTATED DEL PEAK  9(6Q16.1) WILD-TYPE 
                           24                           138 
[1] "DEL PEAK 10(8P22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(8P22) MUTATED DEL PEAK 10(8P22) WILD-TYPE 
                         25                         137 
  DEL PEAK 10(8P22) MUTATED DEL PEAK 10(8P22) WILD-TYPE 
                         25                         137 
[1] "DEL PEAK 11(8Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(8Q23.3) MUTATED DEL PEAK 11(8Q23.3) WILD-TYPE 
                           13                           149 
  DEL PEAK 11(8Q23.3) MUTATED DEL PEAK 11(8Q23.3) WILD-TYPE 
                           13                           149 
[1] "DEL PEAK 12(9P24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(9P24.2) MUTATED DEL PEAK 12(9P24.2) WILD-TYPE 
                           15                           147 
  DEL PEAK 12(9P24.2) MUTATED DEL PEAK 12(9P24.2) WILD-TYPE 
                           15                           147 
[1] "DEL PEAK 13(9Q21.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(9Q21.12) MUTATED DEL PEAK 13(9Q21.12) WILD-TYPE 
                            14                            148 
  DEL PEAK 13(9Q21.12) MUTATED DEL PEAK 13(9Q21.12) WILD-TYPE 
                            14                            148 
[1] "DEL PEAK 14(11P15.4) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(11P15.4) MUTATED DEL PEAK 14(11P15.4) WILD-TYPE 
                            58                            104 
  DEL PEAK 14(11P15.4) MUTATED DEL PEAK 14(11P15.4) WILD-TYPE 
                            58                            104 
[1] "DEL PEAK 15(11Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(11Q22.1) MUTATED DEL PEAK 15(11Q22.1) WILD-TYPE 
                            50                            112 
  DEL PEAK 15(11Q22.1) MUTATED DEL PEAK 15(11Q22.1) WILD-TYPE 
                            50                            112 
[1] "DEL PEAK 16(12Q21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(12Q21.33) MUTATED DEL PEAK 16(12Q21.33) WILD-TYPE 
                              8                             154 
  DEL PEAK 16(12Q21.33) MUTATED DEL PEAK 16(12Q21.33) WILD-TYPE 
                              8                             154 
[1] "DEL PEAK 17(13Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(13Q22.3) MUTATED DEL PEAK 17(13Q22.3) WILD-TYPE 
                             8                            154 
  DEL PEAK 17(13Q22.3) MUTATED DEL PEAK 17(13Q22.3) WILD-TYPE 
                             8                            154 
[1] "DEL PEAK 18(16Q21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(16Q21) MUTATED DEL PEAK 18(16Q21) WILD-TYPE 
                           5                          157 
  DEL PEAK 18(16Q21) MUTATED DEL PEAK 18(16Q21) WILD-TYPE 
                           5                          157 
[1] "DEL PEAK 19(17P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(17P13.2) MUTATED DEL PEAK 19(17P13.2) WILD-TYPE 
                            64                             98 
  DEL PEAK 19(17P13.2) MUTATED DEL PEAK 19(17P13.2) WILD-TYPE 
                            64                             98 
[1] "DEL PEAK 20(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(17Q11.2) MUTATED DEL PEAK 20(17Q11.2) WILD-TYPE 
                            42                            120 
  DEL PEAK 20(17Q11.2) MUTATED DEL PEAK 20(17Q11.2) WILD-TYPE 
                            42                            120 
[1] "DEL PEAK 21(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(22Q13.31) MUTATED DEL PEAK 21(22Q13.31) WILD-TYPE 
                             65                              97 
  DEL PEAK 21(22Q13.31) MUTATED DEL PEAK 21(22Q13.31) WILD-TYPE 
                             65                              97 
[1] "DEL PEAK 22(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(XP21.1) MUTATED DEL PEAK 22(XP21.1) WILD-TYPE 
                           46                           116 
  DEL PEAK 22(XP21.1) MUTATED DEL PEAK 22(XP21.1) WILD-TYPE 
                           46                           116 
[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 = AMP PEAK 1(1Q21.3) MUTATION ANALYSIS
D1V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 1(1Q21.3) MUTATED    26   4
  AMP PEAK 1(1Q21.3) WILD-TYPE 130   2
  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                          30                          132 
  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                           4                            2 
$`AMP PEAK 1(1Q21.3) MUTATED`
TCGA-QR-A70D TCGA-QR-A70P TCGA-SR-A6MV TCGA-WB-A81Q TCGA-WB-A820 TCGA-P7-A5NY 
        0.23       117.14       121.05        24.82        10.16        31.46 
TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A702 TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70X 
      137.59        19.04         1.28         9.01        14.20         6.02 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A686 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
       47.64        37.51        19.30         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SR-A6MS TCGA-SR-A6MZ TCGA-WB-A80L 
       36.56       114.77       109.25        81.93        26.20        34.26 
TCGA-WB-A80P TCGA-WB-A815 TCGA-WB-A819 TCGA-WB-A81G TCGA-WB-A81V TCGA-WB-A81W 
      316.73        53.59        33.90        38.76        71.05        78.21 

$`AMP PEAK 1(1Q21.3) WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A700 TCGA-RW-A68A TCGA-RW-A68B 
       58.88        30.51        14.17        32.15        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-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-XG-A823 TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       20.19        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-A6GY 
       81.70        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-A706 
        9.21         9.93        14.27        31.53        15.58         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-A70N TCGA-QR-A70W TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK 
        1.41        41.79        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-A684 TCGA-RW-A685 
       86.89        19.86         2.93         7.10         1.05         0.85 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-S7-A7WN 
        1.22        27.22         6.28        72.79        11.57        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-A6QF TCGA-SP-A6QG 
       25.32        17.95        24.20         9.73        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-A6MT TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6N0 TCGA-TT-A6YJ 
       68.61       106.75       110.53        24.66        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-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80Q TCGA-WB-A80V 
       41.26         4.47         4.73        25.51       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81F 
       19.59        41.23        42.35        24.16        35.84        57.11 
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-A821 TCGA-WB-A822 
       12.99         1.61        23.77        25.51        93.11       103.17 

  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                        0.23                         0.10 
  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                      316.73                       127.56 
  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                       34.08                        24.03 
[1] "0.2 - 316.7 (34.1)" "0.1 - 127.6 (24.0)"
[1] "hr=" "5.9"
D1V2, continuous
D1V3, binary
                              cls
clus                             0   1
  AMP PEAK 1(1Q21.3) MUTATED    22   8
  AMP PEAK 1(1Q21.3) WILD-TYPE 112  20
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q21.3) MUTATED     22    8
  AMP PEAK 1(1Q21.3) WILD-TYPE  112   20
                    clus
vv                   AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE
  ADRENAL GLAND                              22                          112
  EXTRA-ADRENAL SITE                          8                           20
[1] 2 2
[1] FALSE
D1V4, binary
                              cls
clus                            0  1
  AMP PEAK 1(1Q21.3) MUTATED   13 17
  AMP PEAK 1(1Q21.3) WILD-TYPE 75 57
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q21.3) MUTATED     13   17
  AMP PEAK 1(1Q21.3) WILD-TYPE   75   57
        clus
vv       AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE
  FEMALE                         13                           75
  MALE                           17                           57
[1] 2 2
[1] FALSE
D1V5, binary
                              cls
clus                             0   1
  AMP PEAK 1(1Q21.3) MUTATED    26   4
  AMP PEAK 1(1Q21.3) WILD-TYPE 129   1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q21.3) MUTATED     26    4
  AMP PEAK 1(1Q21.3) WILD-TYPE  129    1
     clus
vv    AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE
  NO                          26                          129
  YES                          4                            1
[1] 2 2
[1] FALSE
D1V6, continuous
                              vv
clus                           PARAGANGLIOMA
  AMP PEAK 1(1Q21.3) MUTATED               5
  AMP PEAK 1(1Q21.3) WILD-TYPE            11
                              vv
clus                           PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  AMP PEAK 1(1Q21.3) MUTATED                                               2
  AMP PEAK 1(1Q21.3) WILD-TYPE                                             9
                              vv
clus                           PHEOCHROMOCYTOMA
  AMP PEAK 1(1Q21.3) MUTATED                 23
  AMP PEAK 1(1Q21.3) WILD-TYPE              112
D1V7, multiclass
                                               clus
vv                                              AMP PEAK 1(1Q21.3) MUTATED
  PARAGANGLIOMA                                                          5
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                          2
  PHEOCHROMOCYTOMA                                                      23
                                               clus
vv                                              AMP PEAK 1(1Q21.3) WILD-TYPE
  PARAGANGLIOMA                                                           11
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                            9
  PHEOCHROMOCYTOMA                                                       112
[1] 3 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
  AMP PEAK 1(1Q21.3) MUTATED                                  0     0
  AMP PEAK 1(1Q21.3) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 1(1Q21.3) MUTATED                           3    26
  AMP PEAK 1(1Q21.3) WILD-TYPE                        16   108
D1V9, multiclass
                                  clus
vv                                 AMP PEAK 1(1Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 3
  WHITE                                                    26
                                  clus
vv                                 AMP PEAK 1(1Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                     108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = AMP PEAK 2(4Q31.1) MUTATION ANALYSIS
D2V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 2(4Q31.1) MUTATED    14   1
  AMP PEAK 2(4Q31.1) WILD-TYPE 142   5
  AMP PEAK 2(4Q31.1) MUTATED AMP PEAK 2(4Q31.1) WILD-TYPE 
                          15                          147 
  AMP PEAK 2(4Q31.1) MUTATED AMP PEAK 2(4Q31.1) WILD-TYPE 
                           1                            5 
$`AMP PEAK 2(4Q31.1) MUTATED`
TCGA-RW-A68G TCGA-P8-A5KC TCGA-PR-A5PF TCGA-PR-A5PH TCGA-QR-A70C TCGA-QR-A70H 
       41.88        29.03        17.95        28.08       116.19        26.83 
TCGA-RW-A686 TCGA-RW-A688 TCGA-SP-A6QI TCGA-TT-A6YN TCGA-W2-A7H5 TCGA-W2-A7HC 
       19.30         1.22       110.04        19.92        20.09        14.43 
TCGA-WB-A80K TCGA-WB-A80Q TCGA-WB-A80Y 
       41.26       127.56        19.59 

$`AMP PEAK 2(4Q31.1) 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-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QR-A6GR 
        4.04        17.75         5.88        81.70        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-A70E 
       14.27        31.53        15.58         1.28         4.11         6.31 
TCGA-QR-A70G TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R 
        2.33        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-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 
        1.05         0.85        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-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-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 
       49.61         4.34        37.35        13.32        42.48        17.16 
TCGA-W2-A7HA TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80L 
        1.18        18.44        16.60        25.61        14.79        34.26 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A815 
        4.47         4.73        25.51       316.73        29.16        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 

  AMP PEAK 2(4Q31.1) MUTATED AMP PEAK 2(4Q31.1) WILD-TYPE 
                        1.22                         0.10 
  AMP PEAK 2(4Q31.1) MUTATED AMP PEAK 2(4Q31.1) WILD-TYPE 
                      127.56                       316.73 
  AMP PEAK 2(4Q31.1) MUTATED AMP PEAK 2(4Q31.1) WILD-TYPE 
                       26.83                        24.82 
[1] "1.2 - 127.6 (26.8)" "0.1 - 316.7 (24.8)"
[1] "hr=" "1.5"
D2V2, continuous
D2V3, binary
                              cls
clus                             0   1
  AMP PEAK 2(4Q31.1) MUTATED    15   0
  AMP PEAK 2(4Q31.1) WILD-TYPE 119  28
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(4Q31.1) MUTATED     15    0
  AMP PEAK 2(4Q31.1) WILD-TYPE  119   28
                    clus
vv                   AMP PEAK 2(4Q31.1) MUTATED AMP PEAK 2(4Q31.1) WILD-TYPE
  ADRENAL GLAND                              15                          119
  EXTRA-ADRENAL SITE                          0                           28
[1] 2 2
[1] FALSE
D2V4, binary
                              cls
clus                            0  1
  AMP PEAK 2(4Q31.1) MUTATED    7  8
  AMP PEAK 2(4Q31.1) WILD-TYPE 81 66
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(4Q31.1) MUTATED      7    8
  AMP PEAK 2(4Q31.1) WILD-TYPE   81   66
        clus
vv       AMP PEAK 2(4Q31.1) MUTATED AMP PEAK 2(4Q31.1) WILD-TYPE
  FEMALE                          7                           81
  MALE                            8                           66
[1] 2 2
[1] FALSE
D2V5, binary
                              cls
clus                             0   1
  AMP PEAK 2(4Q31.1) MUTATED    15   0
  AMP PEAK 2(4Q31.1) WILD-TYPE 140   5
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(4Q31.1) MUTATED     15    0
  AMP PEAK 2(4Q31.1) WILD-TYPE  140    5
     clus
vv    AMP PEAK 2(4Q31.1) MUTATED AMP PEAK 2(4Q31.1) WILD-TYPE
  NO                          15                          140
  YES                          0                            5
[1] 2 2
[1] FALSE
D2V6, continuous
                              vv
clus                           PARAGANGLIOMA
  AMP PEAK 2(4Q31.1) MUTATED               0
  AMP PEAK 2(4Q31.1) WILD-TYPE            16
                              vv
clus                           PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  AMP PEAK 2(4Q31.1) MUTATED                                               0
  AMP PEAK 2(4Q31.1) WILD-TYPE                                            11
                              vv
clus                           PHEOCHROMOCYTOMA
  AMP PEAK 2(4Q31.1) MUTATED                 15
  AMP PEAK 2(4Q31.1) WILD-TYPE              120
D2V7, multiclass
                                               clus
vv                                              AMP PEAK 2(4Q31.1) MUTATED
  PARAGANGLIOMA                                                          0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                          0
  PHEOCHROMOCYTOMA                                                      15
                                               clus
vv                                              AMP PEAK 2(4Q31.1) 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"
D2V8, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 2(4Q31.1) MUTATED                                  0     0
  AMP PEAK 2(4Q31.1) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 2(4Q31.1) MUTATED                           1    14
  AMP PEAK 2(4Q31.1) WILD-TYPE                        18   120
D2V9, multiclass
                                  clus
vv                                 AMP PEAK 2(4Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 1
  WHITE                                                    14
                                  clus
vv                                 AMP PEAK 2(4Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     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(3) Variable = AMP PEAK 3(11P15.2) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 3(11P15.2) MUTATED     8   0
  AMP PEAK 3(11P15.2) WILD-TYPE 148   6
  AMP PEAK 3(11P15.2) MUTATED AMP PEAK 3(11P15.2) WILD-TYPE 
                            8                           154 
  AMP PEAK 3(11P15.2) MUTATED AMP PEAK 3(11P15.2) WILD-TYPE 
                            0                             6 
$`AMP PEAK 3(11P15.2) MUTATED`
TCGA-P8-A5KD TCGA-PR-A5PF TCGA-PR-A5PG TCGA-RW-A689 TCGA-RW-A68D TCGA-SP-A6QF 
        4.04        17.95        81.70        27.22        72.79        82.62 
TCGA-TT-A6YN TCGA-WB-A80O 
       19.92        25.51 

$`AMP PEAK 3(11P15.2) 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-A5PH TCGA-QR-A6GO 
       31.46        29.03        17.75         5.88        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-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-A68C TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        1.22         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-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      114.77       109.25        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-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
      110.53        24.66        26.20        49.61         4.34        37.35 
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-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.47         4.73       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 

  AMP PEAK 3(11P15.2) MUTATED AMP PEAK 3(11P15.2) WILD-TYPE 
                         4.04                          0.10 
  AMP PEAK 3(11P15.2) MUTATED AMP PEAK 3(11P15.2) WILD-TYPE 
                        82.62                        316.73 
  AMP PEAK 3(11P15.2) MUTATED AMP PEAK 3(11P15.2) WILD-TYPE 
                       26.365                        24.740 
[1] "4.0 - 82.6 (26.4)"  "0.1 - 316.7 (24.7)"
[1] "hr="     "2.7e+07"
D3V2, continuous
D3V3, binary
                               cls
clus                              0   1
  AMP PEAK 3(11P15.2) MUTATED     8   0
  AMP PEAK 3(11P15.2) WILD-TYPE 126  28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(11P15.2) MUTATED      8    0
  AMP PEAK 3(11P15.2) WILD-TYPE  126   28
                    clus
vv                   AMP PEAK 3(11P15.2) MUTATED AMP PEAK 3(11P15.2) WILD-TYPE
  ADRENAL GLAND                                8                           126
  EXTRA-ADRENAL SITE                           0                            28
[1] 2 2
[1] FALSE
D3V4, binary
                               cls
clus                             0  1
  AMP PEAK 3(11P15.2) MUTATED    6  2
  AMP PEAK 3(11P15.2) WILD-TYPE 82 72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(11P15.2) MUTATED      6    2
  AMP PEAK 3(11P15.2) WILD-TYPE   82   72
        clus
vv       AMP PEAK 3(11P15.2) MUTATED AMP PEAK 3(11P15.2) WILD-TYPE
  FEMALE                           6                            82
  MALE                             2                            72
[1] 2 2
[1] FALSE
D3V5, binary
                               cls
clus                              0   1
  AMP PEAK 3(11P15.2) MUTATED     8   0
  AMP PEAK 3(11P15.2) WILD-TYPE 147   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(11P15.2) MUTATED      8    0
  AMP PEAK 3(11P15.2) WILD-TYPE  147    5
     clus
vv    AMP PEAK 3(11P15.2) MUTATED AMP PEAK 3(11P15.2) WILD-TYPE
  NO                            8                           147
  YES                           0                             5
[1] 2 2
[1] FALSE
D3V6, continuous
                               vv
clus                            PARAGANGLIOMA
  AMP PEAK 3(11P15.2) MUTATED               0
  AMP PEAK 3(11P15.2) WILD-TYPE            16
                               vv
clus                            PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  AMP PEAK 3(11P15.2) MUTATED                                               0
  AMP PEAK 3(11P15.2) WILD-TYPE                                            11
                               vv
clus                            PHEOCHROMOCYTOMA
  AMP PEAK 3(11P15.2) MUTATED                  8
  AMP PEAK 3(11P15.2) WILD-TYPE              127
D3V7, multiclass
                                               clus
vv                                              AMP PEAK 3(11P15.2) MUTATED
  PARAGANGLIOMA                                                           0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                           0
  PHEOCHROMOCYTOMA                                                        8
                                               clus
vv                                              AMP PEAK 3(11P15.2) 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"
D3V8, continuous
[1] "Remove cluster labels:"      "AMP PEAK 3(11P15.2) MUTATED"
clus
  AMP PEAK 3(11P15.2) MUTATED AMP PEAK 3(11P15.2) WILD-TYPE 
                            1                            17 
                   TCGA-QR-A70D                    TCGA-QR-A70P 
"AMP PEAK 3(11P15.2) WILD-TYPE" "AMP PEAK 3(11P15.2) WILD-TYPE" 
                   TCGA-WB-A814                    TCGA-WB-A820 
"AMP PEAK 3(11P15.2) WILD-TYPE" "AMP PEAK 3(11P15.2) WILD-TYPE" 
                   TCGA-XG-A823                    TCGA-PR-A5PH 
"AMP PEAK 3(11P15.2) WILD-TYPE" "AMP PEAK 3(11P15.2) WILD-TYPE" 
                   TCGA-QR-A702                    TCGA-QT-A5XJ 
"AMP PEAK 3(11P15.2) WILD-TYPE" "AMP PEAK 3(11P15.2) WILD-TYPE" 
                   TCGA-QT-A5XP                    TCGA-QT-A69Q 
"AMP PEAK 3(11P15.2) WILD-TYPE" "AMP PEAK 3(11P15.2) WILD-TYPE" 
                   TCGA-RW-A680                    TCGA-RW-A686 
"AMP PEAK 3(11P15.2) WILD-TYPE" "AMP PEAK 3(11P15.2) WILD-TYPE" 
                   TCGA-RW-A8AZ                    TCGA-TT-A6YK 
"AMP PEAK 3(11P15.2) WILD-TYPE" "AMP PEAK 3(11P15.2) WILD-TYPE" 
                   TCGA-WB-A80Q                    TCGA-WB-A80Y 
"AMP PEAK 3(11P15.2) WILD-TYPE" "AMP PEAK 3(11P15.2) WILD-TYPE" 
                   TCGA-WB-A81W 
"AMP PEAK 3(11P15.2) WILD-TYPE" 
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 3(11P15.2) MUTATED                                  0     2
  AMP PEAK 3(11P15.2) WILD-TYPE                                1     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 3(11P15.2) MUTATED                           0     6
  AMP PEAK 3(11P15.2) WILD-TYPE                        19   128
D3V9, multiclass
                                  clus
vv                                 AMP PEAK 3(11P15.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      6
                                  clus
vv                                 AMP PEAK 3(11P15.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                      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(4) Variable = AMP PEAK 4(12Q13.3) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 4(12Q13.3) MUTATED    16   0
  AMP PEAK 4(12Q13.3) WILD-TYPE 140   6
  AMP PEAK 4(12Q13.3) MUTATED AMP PEAK 4(12Q13.3) WILD-TYPE 
                           16                           146 
  AMP PEAK 4(12Q13.3) MUTATED AMP PEAK 4(12Q13.3) WILD-TYPE 
                            0                             6 
$`AMP PEAK 4(12Q13.3) MUTATED`
TCGA-QR-A6GZ TCGA-QR-A700 TCGA-S7-A7X1 TCGA-W2-A7HB TCGA-QR-A6GX TCGA-QR-A70N 
       30.51        32.15        18.94        19.86        19.04         1.41 
TCGA-QT-A5XJ TCGA-RT-A6YC TCGA-RW-A681 TCGA-RW-A68D TCGA-SR-A6MP TCGA-SR-A6MT 
       36.23         8.09        37.51        72.79        51.22       106.75 
TCGA-SR-A6MZ TCGA-W2-A7H5 TCGA-W2-A7HD TCGA-WB-A821 
       26.20        20.09        18.44        93.11 

$`AMP PEAK 4(12Q13.3) 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-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-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-A5XK TCGA-QT-A5XL 
       41.79         6.02        12.39        17.95         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-RW-A67V TCGA-RW-A67W 
       77.98         0.92       108.26        50.63        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-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
        1.22        27.22         6.28        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-A6MQ TCGA-SR-A6MS 
       15.52       111.25         1.41         0.10        68.61        81.93 
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-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HE 
       13.32        42.48        17.16         1.18        14.43        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-A822 
       78.21       103.17 

  AMP PEAK 4(12Q13.3) MUTATED AMP PEAK 4(12Q13.3) WILD-TYPE 
                         1.41                          0.10 
  AMP PEAK 4(12Q13.3) MUTATED AMP PEAK 4(12Q13.3) WILD-TYPE 
                       106.75                        316.73 
  AMP PEAK 4(12Q13.3) MUTATED AMP PEAK 4(12Q13.3) WILD-TYPE 
                       28.355                        24.740 
[1] "1.4 - 106.8 (28.4)" "0.1 - 316.7 (24.7)"
[1] "hr="     "7.9e+07"
D4V2, continuous
D4V3, binary
                               cls
clus                              0   1
  AMP PEAK 4(12Q13.3) MUTATED    16   0
  AMP PEAK 4(12Q13.3) WILD-TYPE 118  28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(12Q13.3) MUTATED     16    0
  AMP PEAK 4(12Q13.3) WILD-TYPE  118   28
                    clus
vv                   AMP PEAK 4(12Q13.3) MUTATED AMP PEAK 4(12Q13.3) WILD-TYPE
  ADRENAL GLAND                               16                           118
  EXTRA-ADRENAL SITE                           0                            28
[1] 2 2
[1] FALSE
D4V4, binary
                               cls
clus                             0  1
  AMP PEAK 4(12Q13.3) MUTATED    9  7
  AMP PEAK 4(12Q13.3) WILD-TYPE 79 67
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(12Q13.3) MUTATED      9    7
  AMP PEAK 4(12Q13.3) WILD-TYPE   79   67
        clus
vv       AMP PEAK 4(12Q13.3) MUTATED AMP PEAK 4(12Q13.3) WILD-TYPE
  FEMALE                           9                            79
  MALE                             7                            67
[1] 2 2
[1] FALSE
D4V5, binary
                               cls
clus                              0   1
  AMP PEAK 4(12Q13.3) MUTATED    16   0
  AMP PEAK 4(12Q13.3) WILD-TYPE 139   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(12Q13.3) MUTATED     16    0
  AMP PEAK 4(12Q13.3) WILD-TYPE  139    5
     clus
vv    AMP PEAK 4(12Q13.3) MUTATED AMP PEAK 4(12Q13.3) WILD-TYPE
  NO                           16                           139
  YES                           0                             5
[1] 2 2
[1] FALSE
D4V6, continuous
                               vv
clus                            PARAGANGLIOMA
  AMP PEAK 4(12Q13.3) MUTATED               0
  AMP PEAK 4(12Q13.3) WILD-TYPE            16
                               vv
clus                            PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  AMP PEAK 4(12Q13.3) MUTATED                                               0
  AMP PEAK 4(12Q13.3) WILD-TYPE                                            11
                               vv
clus                            PHEOCHROMOCYTOMA
  AMP PEAK 4(12Q13.3) MUTATED                 16
  AMP PEAK 4(12Q13.3) WILD-TYPE              119
D4V7, multiclass
                                               clus
vv                                              AMP PEAK 4(12Q13.3) MUTATED
  PARAGANGLIOMA                                                           0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                           0
  PHEOCHROMOCYTOMA                                                       16
                                               clus
vv                                              AMP PEAK 4(12Q13.3) WILD-TYPE
  PARAGANGLIOMA                                                            16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                            11
  PHEOCHROMOCYTOMA                                                        119
[1] 3 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
[1] "Remove cluster labels:"      "AMP PEAK 4(12Q13.3) MUTATED"
clus
  AMP PEAK 4(12Q13.3) MUTATED AMP PEAK 4(12Q13.3) WILD-TYPE 
                            1                            17 
                   TCGA-QR-A70D                    TCGA-QR-A70P 
"AMP PEAK 4(12Q13.3) WILD-TYPE" "AMP PEAK 4(12Q13.3) WILD-TYPE" 
                   TCGA-WB-A814                    TCGA-WB-A820 
"AMP PEAK 4(12Q13.3) WILD-TYPE" "AMP PEAK 4(12Q13.3) WILD-TYPE" 
                   TCGA-XG-A823                    TCGA-PR-A5PG 
"AMP PEAK 4(12Q13.3) WILD-TYPE" "AMP PEAK 4(12Q13.3) WILD-TYPE" 
                   TCGA-PR-A5PH                    TCGA-QR-A702 
"AMP PEAK 4(12Q13.3) WILD-TYPE" "AMP PEAK 4(12Q13.3) WILD-TYPE" 
                   TCGA-QT-A5XP                    TCGA-QT-A69Q 
"AMP PEAK 4(12Q13.3) WILD-TYPE" "AMP PEAK 4(12Q13.3) WILD-TYPE" 
                   TCGA-RW-A680                    TCGA-RW-A686 
"AMP PEAK 4(12Q13.3) WILD-TYPE" "AMP PEAK 4(12Q13.3) WILD-TYPE" 
                   TCGA-RW-A8AZ                    TCGA-TT-A6YK 
"AMP PEAK 4(12Q13.3) WILD-TYPE" "AMP PEAK 4(12Q13.3) WILD-TYPE" 
                   TCGA-WB-A80Q                    TCGA-WB-A80Y 
"AMP PEAK 4(12Q13.3) WILD-TYPE" "AMP PEAK 4(12Q13.3) WILD-TYPE" 
                   TCGA-WB-A81W 
"AMP PEAK 4(12Q13.3) WILD-TYPE" 
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 4(12Q13.3) MUTATED                                  0     1
  AMP PEAK 4(12Q13.3) WILD-TYPE                                1     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 4(12Q13.3) MUTATED                           3    12
  AMP PEAK 4(12Q13.3) WILD-TYPE                        16   122
D4V9, multiclass
                                  clus
vv                                 AMP PEAK 4(12Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     12
                                  clus
vv                                 AMP PEAK 4(12Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                      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(5) Variable = AMP PEAK 5(14Q24.3) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 5(14Q24.3) MUTATED     9   1
  AMP PEAK 5(14Q24.3) WILD-TYPE 147   5
  AMP PEAK 5(14Q24.3) MUTATED AMP PEAK 5(14Q24.3) WILD-TYPE 
                           10                           152 
  AMP PEAK 5(14Q24.3) MUTATED AMP PEAK 5(14Q24.3) WILD-TYPE 
                            1                             5 
$`AMP PEAK 5(14Q24.3) MUTATED`
TCGA-QR-A700 TCGA-WB-A820 TCGA-QR-A70N TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A5XN 
       32.15        10.16         1.41        36.23         1.81        25.18 
TCGA-QT-A5XO TCGA-RW-A681 TCGA-S7-A7WT TCGA-SR-A6MT 
        2.30        37.51        42.77       106.75 

$`AMP PEAK 5(14Q24.3) 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-XG-A823 TCGA-P7-A5NY TCGA-P8-A5KC 
       43.07        48.53        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-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-A5XK TCGA-QT-A5XM TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
       17.95         6.94         0.72         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-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       31.04        40.70        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 

  AMP PEAK 5(14Q24.3) MUTATED AMP PEAK 5(14Q24.3) WILD-TYPE 
                         1.41                          0.10 
  AMP PEAK 5(14Q24.3) MUTATED AMP PEAK 5(14Q24.3) WILD-TYPE 
                       106.75                        316.73 
  AMP PEAK 5(14Q24.3) MUTATED AMP PEAK 5(14Q24.3) WILD-TYPE 
                       28.665                        24.740 
[1] "1.4 - 106.8 (28.7)" "0.1 - 316.7 (24.7)"
[1] "hr=" "4.1"
D5V2, continuous
D5V3, binary
                               cls
clus                              0   1
  AMP PEAK 5(14Q24.3) MUTATED    10   0
  AMP PEAK 5(14Q24.3) WILD-TYPE 124  28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 5(14Q24.3) MUTATED     10    0
  AMP PEAK 5(14Q24.3) WILD-TYPE  124   28
                    clus
vv                   AMP PEAK 5(14Q24.3) MUTATED AMP PEAK 5(14Q24.3) WILD-TYPE
  ADRENAL GLAND                               10                           124
  EXTRA-ADRENAL SITE                           0                            28
[1] 2 2
[1] FALSE
D5V4, binary
                               cls
clus                             0  1
  AMP PEAK 5(14Q24.3) MUTATED    4  6
  AMP PEAK 5(14Q24.3) WILD-TYPE 84 68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 5(14Q24.3) MUTATED      4    6
  AMP PEAK 5(14Q24.3) WILD-TYPE   84   68
        clus
vv       AMP PEAK 5(14Q24.3) MUTATED AMP PEAK 5(14Q24.3) WILD-TYPE
  FEMALE                           4                            84
  MALE                             6                            68
[1] 2 2
[1] FALSE
D5V5, binary
                               cls
clus                              0   1
  AMP PEAK 5(14Q24.3) MUTATED    10   0
  AMP PEAK 5(14Q24.3) WILD-TYPE 145   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 5(14Q24.3) MUTATED     10    0
  AMP PEAK 5(14Q24.3) WILD-TYPE  145    5
     clus
vv    AMP PEAK 5(14Q24.3) MUTATED AMP PEAK 5(14Q24.3) WILD-TYPE
  NO                           10                           145
  YES                           0                             5
[1] 2 2
[1] FALSE
D5V6, continuous
[1] "Remove cluster labels:"      "AMP PEAK 5(14Q24.3) MUTATED"
clus
  AMP PEAK 5(14Q24.3) MUTATED AMP PEAK 5(14Q24.3) WILD-TYPE 
                            1                            59 
                   TCGA-S7-A7WQ                    TCGA-S7-A7WU 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-S7-A7X1                    TCGA-SR-A6MV 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-WB-A817                    TCGA-WB-A81E 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-XG-A823                    TCGA-P7-A5NY 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-PR-A5PF                    TCGA-PR-A5PG 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-PR-A5PH                    TCGA-RT-A6YA 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-RT-A6YC                    TCGA-RX-A8JQ 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-S7-A7WL                    TCGA-S7-A7WM 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-S7-A7WN                    TCGA-S7-A7WO 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-S7-A7WP                    TCGA-S7-A7WR 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-S7-A7WV                    TCGA-S7-A7WW 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-S7-A7WX                    TCGA-S7-A7X0 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-S7-A7X2                    TCGA-SP-A6QC 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-SP-A6QD                    TCGA-SP-A6QF 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-SP-A6QG                    TCGA-SP-A6QI 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-SP-A6QJ                    TCGA-SP-A6QK 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-SR-A6MQ                    TCGA-SR-A6MS 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-SR-A6MY                    TCGA-SR-A6MZ 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-SR-A6N0                    TCGA-TT-A6YK 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-TT-A6YN                    TCGA-TT-A6YO 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-TT-A6YP                    TCGA-WB-A80K 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-WB-A80L                    TCGA-WB-A80Q 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-WB-A815                    TCGA-WB-A818 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-WB-A81D                    TCGA-WB-A81F 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-WB-A81G                    TCGA-WB-A81H 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-WB-A81I                    TCGA-WB-A81J 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-WB-A81K                    TCGA-WB-A81M 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-WB-A81N                    TCGA-WB-A81S 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-WB-A81T                    TCGA-WB-A821 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-WB-A822 
"AMP PEAK 5(14Q24.3) WILD-TYPE" 
                               vv
clus                            PARAGANGLIOMA
  AMP PEAK 5(14Q24.3) MUTATED               0
  AMP PEAK 5(14Q24.3) WILD-TYPE            16
                               vv
clus                            PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  AMP PEAK 5(14Q24.3) MUTATED                                               0
  AMP PEAK 5(14Q24.3) WILD-TYPE                                            11
                               vv
clus                            PHEOCHROMOCYTOMA
  AMP PEAK 5(14Q24.3) MUTATED                 10
  AMP PEAK 5(14Q24.3) WILD-TYPE              125
D5V7, multiclass
                                               clus
vv                                              AMP PEAK 5(14Q24.3) MUTATED
  PARAGANGLIOMA                                                           0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                           0
  PHEOCHROMOCYTOMA                                                       10
                                               clus
vv                                              AMP PEAK 5(14Q24.3) 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"
D5V8, continuous
[1] "Remove cluster labels:"      "AMP PEAK 5(14Q24.3) MUTATED"
clus
  AMP PEAK 5(14Q24.3) MUTATED AMP PEAK 5(14Q24.3) WILD-TYPE 
                            2                            16 
                   TCGA-QR-A70D                    TCGA-QR-A70P 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-WB-A814                    TCGA-XG-A823 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-PR-A5PG                    TCGA-PR-A5PH 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-QR-A702                    TCGA-QT-A5XP 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-QT-A69Q                    TCGA-RW-A680 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-RW-A686                    TCGA-RW-A8AZ 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-TT-A6YK                    TCGA-WB-A80Q 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                   TCGA-WB-A80Y                    TCGA-WB-A81W 
"AMP PEAK 5(14Q24.3) WILD-TYPE" "AMP PEAK 5(14Q24.3) WILD-TYPE" 
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 5(14Q24.3) MUTATED                                  0     0
  AMP PEAK 5(14Q24.3) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 5(14Q24.3) MUTATED                           4     6
  AMP PEAK 5(14Q24.3) WILD-TYPE                        15   128
D5V9, multiclass
                                  clus
vv                                 AMP PEAK 5(14Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                      6
                                  clus
vv                                 AMP PEAK 5(14Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   15
  WHITE                                                      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(6) Variable = AMP PEAK 6(17Q21.31) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 6(17Q21.31) MUTATED    14   2
  AMP PEAK 6(17Q21.31) WILD-TYPE 142   4
  AMP PEAK 6(17Q21.31) MUTATED AMP PEAK 6(17Q21.31) WILD-TYPE 
                            16                            146 
  AMP PEAK 6(17Q21.31) MUTATED AMP PEAK 6(17Q21.31) WILD-TYPE 
                             2                              4 
$`AMP PEAK 6(17Q21.31) MUTATED`
TCGA-WB-A81Q TCGA-P8-A5KC TCGA-PR-A5PF TCGA-PR-A5PH TCGA-QR-A70C TCGA-QR-A70H 
       24.82        29.03        17.95        28.08       116.19        26.83 
TCGA-QR-A70K TCGA-RW-A681 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A8AZ TCGA-WB-A80K 
        9.01        37.51        19.30         1.22         2.89        41.26 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A81J TCGA-WB-A81W 
      316.73       127.56        24.36        78.21 

$`AMP PEAK 6(17Q21.31) 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-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QR-A6GR 
        4.04        17.75         5.88        81.70        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-A70E 
       14.27        31.53        15.58         1.28         4.11         6.31 
TCGA-QR-A70G TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W 
        2.33        29.92        13.12         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-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RX-A8JQ TCGA-S7-A7WL 
       27.22         6.28        72.79        11.57        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-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80V TCGA-WB-A80Y 
       34.26         4.47         4.73        25.51        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-A821 TCGA-WB-A822 
       93.11       103.17 

  AMP PEAK 6(17Q21.31) MUTATED AMP PEAK 6(17Q21.31) WILD-TYPE 
                          1.22                           0.10 
  AMP PEAK 6(17Q21.31) MUTATED AMP PEAK 6(17Q21.31) WILD-TYPE 
                        316.73                         137.59 
  AMP PEAK 6(17Q21.31) MUTATED AMP PEAK 6(17Q21.31) WILD-TYPE 
                        27.455                         24.430 
[1] "1.2 - 316.7 (27.5)" "0.1 - 137.6 (24.4)"
[1] "hr=" "3"  
D6V2, continuous
D6V3, binary
                                cls
clus                               0   1
  AMP PEAK 6(17Q21.31) MUTATED    15   1
  AMP PEAK 6(17Q21.31) WILD-TYPE 119  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 6(17Q21.31) MUTATED     15    1
  AMP PEAK 6(17Q21.31) WILD-TYPE  119   27
                    clus
vv                   AMP PEAK 6(17Q21.31) MUTATED
  ADRENAL GLAND                                15
  EXTRA-ADRENAL SITE                            1
                    clus
vv                   AMP PEAK 6(17Q21.31) WILD-TYPE
  ADRENAL GLAND                                 119
  EXTRA-ADRENAL SITE                             27
[1] 2 2
[1] FALSE
D6V4, binary
                                cls
clus                              0  1
  AMP PEAK 6(17Q21.31) MUTATED    4 12
  AMP PEAK 6(17Q21.31) WILD-TYPE 84 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 6(17Q21.31) MUTATED      4   12
  AMP PEAK 6(17Q21.31) WILD-TYPE   84   62
        clus
vv       AMP PEAK 6(17Q21.31) MUTATED AMP PEAK 6(17Q21.31) WILD-TYPE
  FEMALE                            4                             84
  MALE                             12                             62
[1] 2 2
[1] FALSE
D6V5, binary
                                cls
clus                               0   1
  AMP PEAK 6(17Q21.31) MUTATED    14   2
  AMP PEAK 6(17Q21.31) WILD-TYPE 141   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 6(17Q21.31) MUTATED     14    2
  AMP PEAK 6(17Q21.31) WILD-TYPE  141    3
     clus
vv    AMP PEAK 6(17Q21.31) MUTATED AMP PEAK 6(17Q21.31) WILD-TYPE
  NO                            14                            141
  YES                            2                              3
[1] 2 2
[1] FALSE
D6V6, continuous
                                vv
clus                             PARAGANGLIOMA
  AMP PEAK 6(17Q21.31) MUTATED               0
  AMP PEAK 6(17Q21.31) WILD-TYPE            16
                                vv
clus                             PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  AMP PEAK 6(17Q21.31) MUTATED                                               1
  AMP PEAK 6(17Q21.31) WILD-TYPE                                            10
                                vv
clus                             PHEOCHROMOCYTOMA
  AMP PEAK 6(17Q21.31) MUTATED                 15
  AMP PEAK 6(17Q21.31) WILD-TYPE              120
D6V7, multiclass
                                               clus
vv                                              AMP PEAK 6(17Q21.31) MUTATED
  PARAGANGLIOMA                                                            0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                            1
  PHEOCHROMOCYTOMA                                                        15
                                               clus
vv                                              AMP PEAK 6(17Q21.31) WILD-TYPE
  PARAGANGLIOMA                                                             16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                             10
  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"
D6V8, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 6(17Q21.31) MUTATED                                  0     0
  AMP PEAK 6(17Q21.31) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 6(17Q21.31) MUTATED                           1    15
  AMP PEAK 6(17Q21.31) WILD-TYPE                        18   119
D6V9, multiclass
                                  clus
vv                                 AMP PEAK 6(17Q21.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      15
                                  clus
vv                                 AMP PEAK 6(17Q21.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    18
  WHITE                                                       119
[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 = DEL PEAK  1(1P12) MUTATION ANALYSIS
D7V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  1(1P12) MUTATED   109   4
  DEL PEAK  1(1P12) WILD-TYPE  47   2
  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                        113                          49 
  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                          4                           2 
$`DEL PEAK  1(1P12) 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-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       26.96        18.94       121.05         3.12        19.86        17.69 
TCGA-WB-A81E TCGA-WB-A820 TCGA-P7-A5NY TCGA-P8-A5KD TCGA-P8-A6RX TCGA-PR-A5PF 
       48.53        10.16        31.46         4.04        17.75        17.95 
TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX 
       81.70        35.01        23.11         1.25       137.59        19.04 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A70E TCGA-QR-A70H 
        9.93        14.27        15.58         1.28         6.31        26.83 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A7IN TCGA-QR-A7IP 
       13.12         9.01        14.20        41.79        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A5XP 
       36.23         6.94         1.81         0.72         2.30         4.41 
TCGA-QT-A69Q TCGA-RM-A68T TCGA-RT-A6YA TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67Y 
        0.79        77.98        50.63        86.89        19.86         7.10 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 
       47.64        37.51         1.05         0.85         1.22        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-A7WR TCGA-S7-A7WT TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 
       37.25        40.70        42.77        25.32        17.95        24.20 
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-A6MT 
      111.25         1.41        51.22        68.61        81.93       106.75 
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-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7UY 
       20.09        17.16         1.18        14.43        18.44        14.79 
TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80V 
       41.26         4.47         4.73        25.51       316.73        29.16 
TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G 
       41.23        42.35        33.90        35.84        57.11        38.76 
TCGA-WB-A81H TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S 
       63.98        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 

$`DEL PEAK  1(1P12) 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-WB-A814 TCGA-WB-A817 TCGA-WB-A81Q TCGA-XG-A823 TCGA-P8-A5KC TCGA-P8-A6RY 
       74.04        43.07        24.82        20.19        29.03         5.88 
TCGA-PR-A5PH TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H5 TCGA-QR-A706 TCGA-QR-A70C 
       28.08         1.05         9.21        31.53         4.11       116.19 
TCGA-QR-A70G TCGA-QR-A70I TCGA-QR-A70N TCGA-QR-A70X TCGA-QT-A5XN TCGA-QT-A7U0 
        2.33        29.92         1.41         6.02        25.18        13.08 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67X TCGA-RW-A686 TCGA-RW-A68C 
        0.92       108.26         8.09         2.93        19.30         6.28 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WV TCGA-S7-A7WW TCGA-SA-A6C2 TCGA-SQ-A6I6 
       35.51        31.04        27.91        23.21         9.73         0.10 
TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HE TCGA-W2-A7HH TCGA-WB-A80L 
       49.61        13.32        42.48        16.60        25.61        34.26 
TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A81A TCGA-WB-A81I TCGA-WB-A81J 
      127.56        19.59        53.59        24.16        22.32        24.36 
TCGA-WB-A81N 
       62.04 

  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                       0.23                        0.10 
  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                     316.73                      127.56 
  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                      25.05                       24.82 
[1] "0.2 - 316.7 (25.1)" "0.1 - 127.6 (24.8)"
[1] "hr=" "1.2"
D7V2, continuous
D7V3, binary
                             cls
clus                           0  1
  DEL PEAK  1(1P12) MUTATED   94 19
  DEL PEAK  1(1P12) WILD-TYPE 40  9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  1(1P12) MUTATED     94   19
  DEL PEAK  1(1P12) WILD-TYPE   40    9
                    clus
vv                   DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE
  ADRENAL GLAND                             94                          40
  EXTRA-ADRENAL SITE                        19                           9
[1] 2 2
[1] FALSE
D7V4, binary
                             cls
clus                           0  1
  DEL PEAK  1(1P12) MUTATED   61 52
  DEL PEAK  1(1P12) WILD-TYPE 27 22
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  1(1P12) MUTATED     61   52
  DEL PEAK  1(1P12) WILD-TYPE   27   22
        clus
vv       DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE
  FEMALE                        61                          27
  MALE                          52                          22
[1] 2 2
[1] FALSE
D7V5, binary
                             cls
clus                            0   1
  DEL PEAK  1(1P12) MUTATED   108   4
  DEL PEAK  1(1P12) WILD-TYPE  47   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  1(1P12) MUTATED    108    4
  DEL PEAK  1(1P12) WILD-TYPE   47    1
     clus
vv    DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE
  NO                        108                          47
  YES                         4                           1
[1] 2 2
[1] FALSE
D7V6, continuous
                             vv
clus                          PARAGANGLIOMA
  DEL PEAK  1(1P12) MUTATED              13
  DEL PEAK  1(1P12) WILD-TYPE             3
                             vv
clus                          PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK  1(1P12) MUTATED                                               5
  DEL PEAK  1(1P12) WILD-TYPE                                             6
                             vv
clus                          PHEOCHROMOCYTOMA
  DEL PEAK  1(1P12) MUTATED                 95
  DEL PEAK  1(1P12) WILD-TYPE               40
D7V7, multiclass
                                               clus
vv                                              DEL PEAK  1(1P12) MUTATED
  PARAGANGLIOMA                                                        13
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                         5
  PHEOCHROMOCYTOMA                                                     95
                                               clus
vv                                              DEL PEAK  1(1P12) WILD-TYPE
  PARAGANGLIOMA                                                           3
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                           6
  PHEOCHROMOCYTOMA                                                       40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P12) MUTATED                                  1     5
  DEL PEAK  1(1P12) WILD-TYPE                                0     0
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P12) MUTATED                           9    95
  DEL PEAK  1(1P12) WILD-TYPE                        10    39
D7V9, multiclass
                                  clus
vv                                 DEL PEAK  1(1P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    5
  BLACK OR AFRICAN AMERICAN                                9
  WHITE                                                   95
                                  clus
vv                                 DEL PEAK  1(1P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                     39
[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 = DEL PEAK  2(1Q44) MUTATION ANALYSIS
D8V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  2(1Q44) MUTATED    19   2
  DEL PEAK  2(1Q44) WILD-TYPE 137   4
  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                         21                         141 
  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                          2                           4 
$`DEL PEAK  2(1Q44) MUTATED`
TCGA-QR-A700 TCGA-RW-A68A TCGA-S7-A7WQ TCGA-S7-A7X1 TCGA-WB-A81E TCGA-WB-A820 
       32.15        25.05        26.96        18.94        48.53        10.16 
TCGA-QR-A6H3 TCGA-QR-A70E TCGA-QR-A70X TCGA-QR-A7IN TCGA-QT-A69Q TCGA-RM-A68T 
       14.27         6.31         6.02        12.39         0.79        77.98 
TCGA-RW-A681 TCGA-RW-A8AZ TCGA-SR-A6MT TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-W2-A7H7 
       37.51         2.89       106.75        24.66         4.34        17.16 
TCGA-WB-A81F TCGA-WB-A81K TCGA-WB-A821 
       57.11        40.04        93.11 

$`DEL PEAK  2(1Q44) 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-A7WU TCGA-SR-A6MV TCGA-SR-A6MX 
       44.52        41.88        13.87        30.51       121.05         3.12 
TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81Q TCGA-XG-A823 
       19.86        17.69        74.04        43.07        24.82        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-A6H5 TCGA-QR-A6H6 
       19.04         1.05         9.21         9.93        31.53        15.58 
TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A70C TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
        1.28         4.11       116.19         2.33        26.83        29.92 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A7IP 
       13.12         9.01         1.41        14.20        41.79        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-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC 
        4.41        13.08         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-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-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-A6MZ TCGA-SR-A6N0 
       51.22        68.61        81.93       110.53        26.20        49.61 
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-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-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       24.16        35.84        38.76        63.98        22.32        24.36 
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 

  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                       0.79                        0.10 
  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                     106.75                      316.73 
  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                      24.66                       25.18 
[1] "0.8 - 106.8 (24.7)" "0.1 - 316.7 (25.2)"
[1] "hr=" "4.6"
D8V2, continuous
D8V3, binary
                             cls
clus                            0   1
  DEL PEAK  2(1Q44) MUTATED    18   3
  DEL PEAK  2(1Q44) WILD-TYPE 116  25
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q44) MUTATED     18    3
  DEL PEAK  2(1Q44) WILD-TYPE  116   25
                    clus
vv                   DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE
  ADRENAL GLAND                             18                         116
  EXTRA-ADRENAL SITE                         3                          25
[1] 2 2
[1] FALSE
D8V4, binary
                             cls
clus                           0  1
  DEL PEAK  2(1Q44) MUTATED    9 12
  DEL PEAK  2(1Q44) WILD-TYPE 79 62
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q44) MUTATED      9   12
  DEL PEAK  2(1Q44) WILD-TYPE   79   62
        clus
vv       DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE
  FEMALE                         9                          79
  MALE                          12                          62
[1] 2 2
[1] FALSE
D8V5, binary
                             cls
clus                            0   1
  DEL PEAK  2(1Q44) MUTATED    21   0
  DEL PEAK  2(1Q44) WILD-TYPE 134   5
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q44) MUTATED     21    0
  DEL PEAK  2(1Q44) WILD-TYPE  134    5
     clus
vv    DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE
  NO                         21                         134
  YES                         0                           5
[1] 2 2
[1] FALSE
D8V6, continuous
                             vv
clus                          PARAGANGLIOMA
  DEL PEAK  2(1Q44) MUTATED               2
  DEL PEAK  2(1Q44) WILD-TYPE            14
                             vv
clus                          PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK  2(1Q44) MUTATED                                               1
  DEL PEAK  2(1Q44) WILD-TYPE                                            10
                             vv
clus                          PHEOCHROMOCYTOMA
  DEL PEAK  2(1Q44) MUTATED                 18
  DEL PEAK  2(1Q44) WILD-TYPE              117
D8V7, multiclass
                                               clus
vv                                              DEL PEAK  2(1Q44) MUTATED
  PARAGANGLIOMA                                                         2
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                         1
  PHEOCHROMOCYTOMA                                                     18
                                               clus
vv                                              DEL PEAK  2(1Q44) 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"
D8V8, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1Q44) MUTATED                                  0     0
  DEL PEAK  2(1Q44) WILD-TYPE                                1     5
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1Q44) MUTATED                           3    17
  DEL PEAK  2(1Q44) WILD-TYPE                        16   117
D8V9, multiclass
                                  clus
vv                                 DEL PEAK  2(1Q44) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                3
  WHITE                                                   17
                                  clus
vv                                 DEL PEAK  2(1Q44) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                    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(9) Variable = DEL PEAK  3(3P24.1) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  3(3P24.1) MUTATED   62  2
  DEL PEAK  3(3P24.1) WILD-TYPE 94  4
  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                           64                            98 
  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                            2                             4 
$`DEL PEAK  3(3P24.1) 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-A81E TCGA-XG-A823 TCGA-P8-A6RX TCGA-PR-A5PF TCGA-QR-A6GT TCGA-QR-A6GY 
       48.53        20.19        17.75        17.95       137.59         1.05 
TCGA-QR-A6H5 TCGA-QR-A706 TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70X 
       31.53         4.11        13.12         1.41        14.20         6.02 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XN 
       12.39        17.95        36.23         6.94         1.81        25.18 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A689 
      108.26        50.63         2.93         7.10        47.64        27.22 
TCGA-RW-A68C TCGA-RW-A68D TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WP TCGA-S7-A7WR 
        6.28        72.79        31.59        36.56        31.04        40.70 
TCGA-S7-A7WT TCGA-S7-A7X0 TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SQ-A6I6 TCGA-SR-A6MT 
       42.77        17.95       109.25        79.46         0.10       106.75 
TCGA-SR-A6MU TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
      110.53         4.34        37.35        42.48        20.09        17.16 
TCGA-W2-A7HA TCGA-W2-A7UY TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 
        1.18        14.79       316.73        29.16        19.59        53.59 
TCGA-WB-A819 TCGA-WB-A81K TCGA-WB-A81W TCGA-WB-A821 
       33.90        40.04        78.21        93.11 

$`DEL PEAK  3(3P24.1) 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-A81Q TCGA-WB-A820 TCGA-P7-A5NY TCGA-P8-A5KC 
       19.86        43.07        24.82        10.16        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-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I 
        1.28       116.19         6.31         2.33        26.83        29.92 
TCGA-QR-A70K TCGA-QR-A70W TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q 
        9.01        41.79         0.72         2.30         4.41         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-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A7D0 
       37.51         1.05         0.85        19.30         1.22        11.57 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WV TCGA-S7-A7WW 
        2.89        20.09        37.25        35.51        27.91        23.21 
TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QI 
       25.32        24.20         9.73       114.77        82.62       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
       15.52       111.25         1.41        51.22        68.61        81.93 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7HC 
       24.66        26.20        49.61        19.92        13.32        14.43 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       18.44        16.60        25.61        41.26        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80Q TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A81A 
        4.73        25.51       127.56        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-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 

  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                         0.10                          0.72 
  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                       316.73                        127.56 
  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                        28.19                         24.18 
[1] "0.1 - 316.7 (28.2)" "0.7 - 127.6 (24.2)"
[1] "hr=" "1.9"
D9V2, continuous
D9V3, binary
                               cls
clus                             0  1
  DEL PEAK  3(3P24.1) MUTATED   49 15
  DEL PEAK  3(3P24.1) WILD-TYPE 85 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(3P24.1) MUTATED     49   15
  DEL PEAK  3(3P24.1) WILD-TYPE   85   13
                    clus
vv                   DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE
  ADRENAL GLAND                               49                            85
  EXTRA-ADRENAL SITE                          15                            13
[1] 2 2
[1] FALSE
D9V4, binary
                               cls
clus                             0  1
  DEL PEAK  3(3P24.1) MUTATED   40 24
  DEL PEAK  3(3P24.1) WILD-TYPE 48 50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(3P24.1) MUTATED     40   24
  DEL PEAK  3(3P24.1) WILD-TYPE   48   50
        clus
vv       DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE
  FEMALE                          40                            48
  MALE                            24                            50
[1] 2 2
[1] FALSE
D9V5, binary
                               cls
clus                             0  1
  DEL PEAK  3(3P24.1) MUTATED   60  3
  DEL PEAK  3(3P24.1) WILD-TYPE 95  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(3P24.1) MUTATED     60    3
  DEL PEAK  3(3P24.1) WILD-TYPE   95    2
     clus
vv    DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE
  NO                           60                            95
  YES                           3                             2
[1] 2 2
[1] FALSE
D9V6, continuous
                               vv
clus                            PARAGANGLIOMA
  DEL PEAK  3(3P24.1) MUTATED               7
  DEL PEAK  3(3P24.1) WILD-TYPE             9
                               vv
clus                            PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK  3(3P24.1) MUTATED                                               7
  DEL PEAK  3(3P24.1) WILD-TYPE                                             4
                               vv
clus                            PHEOCHROMOCYTOMA
  DEL PEAK  3(3P24.1) MUTATED                 50
  DEL PEAK  3(3P24.1) WILD-TYPE               85
D9V7, multiclass
                                               clus
vv                                              DEL PEAK  3(3P24.1) MUTATED
  PARAGANGLIOMA                                                           7
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                           7
  PHEOCHROMOCYTOMA                                                       50
                                               clus
vv                                              DEL PEAK  3(3P24.1) WILD-TYPE
  PARAGANGLIOMA                                                             9
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                             4
  PHEOCHROMOCYTOMA                                                         85
[1] 3 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
  DEL PEAK  3(3P24.1) MUTATED                                  1     1
  DEL PEAK  3(3P24.1) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(3P24.1) MUTATED                          10    50
  DEL PEAK  3(3P24.1) WILD-TYPE                         9    84
D9V9, multiclass
                                  clus
vv                                 DEL PEAK  3(3P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                     50
                                  clus
vv                                 DEL PEAK  3(3P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                       84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = DEL PEAK  4(3Q26.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(3Q26.1) MUTATED   91  2
  DEL PEAK  4(3Q26.1) WILD-TYPE 65  4
  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                           93                            69 
  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                            2                             4 
$`DEL PEAK  4(3Q26.1) 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-A5XO 
       17.95        36.23         6.94         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
        4.41       108.26        50.63        19.86         2.93         7.10 
TCGA-RW-A680 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A7D0 
       47.64         0.85         1.22        27.22         6.28        11.57 
TCGA-S7-A7WL TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 
       31.59        31.04        40.70        25.32        17.95        24.20 
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-A6MU 
        1.41         0.10        51.22        68.61       106.75       110.53 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YP 
       24.66        26.20         4.34        37.35        19.92        42.48 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7UY 
       20.09        17.16         1.18        14.43        18.44        14.79 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A816 TCGA-WB-A818 
        4.47         4.73       316.73        29.16        41.23        42.35 
TCGA-WB-A819 TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       33.90        57.11        38.76         1.61        23.77        25.51 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       78.21        93.11       103.17 

$`DEL PEAK  4(3Q26.1) 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-A69Q TCGA-QT-A7U0 
       29.92         9.01         6.02         1.81         0.79        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A681 TCGA-RW-A684 
       77.98         0.92         8.09        86.89        37.51         1.05 
TCGA-RW-A686 TCGA-RW-A68D TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN 
       19.30        72.79         2.89        20.09        36.56        37.25 
TCGA-S7-A7WO TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-SA-A6C2 TCGA-SP-A6QC 
       35.51        42.77        27.91        23.21         9.73       114.77 
TCGA-SR-A6MS TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-W2-A7HE TCGA-W2-A7HH TCGA-WB-A80K 
       81.93        49.61        13.32        16.60        25.61        41.26 
TCGA-WB-A80L TCGA-WB-A80O TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A81A 
       34.26        25.51       127.56        19.59        53.59        24.16 
TCGA-WB-A81D TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       35.84        63.98        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81V 
       62.04        12.99        71.05 

  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                         0.10                          0.79 
  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                       316.73                        127.56 
  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                        23.90                         26.83 
[1] "0.1 - 316.7 (23.9)" "0.8 - 127.6 (26.8)"
[1] "hr=" "2.6"
D10V2, continuous
D10V3, binary
                               cls
clus                             0  1
  DEL PEAK  4(3Q26.1) MUTATED   76 17
  DEL PEAK  4(3Q26.1) WILD-TYPE 58 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3Q26.1) MUTATED     76   17
  DEL PEAK  4(3Q26.1) WILD-TYPE   58   11
                    clus
vv                   DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE
  ADRENAL GLAND                               76                            58
  EXTRA-ADRENAL SITE                          17                            11
[1] 2 2
[1] FALSE
D10V4, binary
                               cls
clus                             0  1
  DEL PEAK  4(3Q26.1) MUTATED   51 42
  DEL PEAK  4(3Q26.1) WILD-TYPE 37 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3Q26.1) MUTATED     51   42
  DEL PEAK  4(3Q26.1) WILD-TYPE   37   32
        clus
vv       DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE
  FEMALE                          51                            37
  MALE                            42                            32
[1] 2 2
[1] FALSE
D10V5, binary
                               cls
clus                             0  1
  DEL PEAK  4(3Q26.1) MUTATED   88  3
  DEL PEAK  4(3Q26.1) WILD-TYPE 67  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3Q26.1) MUTATED     88    3
  DEL PEAK  4(3Q26.1) WILD-TYPE   67    2
     clus
vv    DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE
  NO                           88                            67
  YES                           3                             2
[1] 2 2
[1] FALSE
D10V6, continuous
                               vv
clus                            PARAGANGLIOMA
  DEL PEAK  4(3Q26.1) MUTATED               9
  DEL PEAK  4(3Q26.1) WILD-TYPE             7
                               vv
clus                            PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK  4(3Q26.1) MUTATED                                               7
  DEL PEAK  4(3Q26.1) WILD-TYPE                                             4
                               vv
clus                            PHEOCHROMOCYTOMA
  DEL PEAK  4(3Q26.1) MUTATED                 77
  DEL PEAK  4(3Q26.1) WILD-TYPE               58
D10V7, multiclass
                                               clus
vv                                              DEL PEAK  4(3Q26.1) MUTATED
  PARAGANGLIOMA                                                           9
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                           7
  PHEOCHROMOCYTOMA                                                       77
                                               clus
vv                                              DEL PEAK  4(3Q26.1) WILD-TYPE
  PARAGANGLIOMA                                                             7
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                             4
  PHEOCHROMOCYTOMA                                                         58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(3Q26.1) MUTATED                                  1     3
  DEL PEAK  4(3Q26.1) WILD-TYPE                                0     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(3Q26.1) MUTATED                          11    75
  DEL PEAK  4(3Q26.1) WILD-TYPE                         8    59
D10V9, multiclass
                                  clus
vv                                 DEL PEAK  4(3Q26.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                     75
                                  clus
vv                                 DEL PEAK  4(3Q26.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                       59
[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 = DEL PEAK  5(4Q22.1) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(4Q22.1) MUTATED    13   0
  DEL PEAK  5(4Q22.1) WILD-TYPE 143   6
  DEL PEAK  5(4Q22.1) MUTATED DEL PEAK  5(4Q22.1) WILD-TYPE 
                           13                           149 
  DEL PEAK  5(4Q22.1) MUTATED DEL PEAK  5(4Q22.1) WILD-TYPE 
                            0                             6 
$`DEL PEAK  5(4Q22.1) MUTATED`
TCGA-QR-A700 TCGA-QR-A70N TCGA-QR-A70R TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RM-A68W 
       32.15         1.41        14.20         2.30         0.79         0.92 
TCGA-RT-A6YA TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A68C TCGA-TT-A6YP TCGA-WB-A81T 
       50.63        19.86         2.93         6.28        42.48        25.51 
TCGA-WB-A821 
       93.11 

$`DEL PEAK  5(4Q22.1) 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-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-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V 
        4.41        13.08        77.98       108.26         8.09        86.89 
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-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
        1.22        27.22        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-W2-A7H5 TCGA-W2-A7H7 
        4.34        37.35        19.92        13.32        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-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-A81V TCGA-WB-A81W TCGA-WB-A822 
        1.61        23.77        71.05        78.21       103.17 

  DEL PEAK  5(4Q22.1) MUTATED DEL PEAK  5(4Q22.1) WILD-TYPE 
                         0.79                          0.10 
  DEL PEAK  5(4Q22.1) MUTATED DEL PEAK  5(4Q22.1) WILD-TYPE 
                        93.11                        316.73 
  DEL PEAK  5(4Q22.1) MUTATED DEL PEAK  5(4Q22.1) WILD-TYPE 
                        14.20                         25.18 
[1] "0.8 - 93.1 (14.2)"  "0.1 - 316.7 (25.2)"
[1] "hr="     "2.7e+07"
D11V2, continuous
D11V3, binary
                               cls
clus                              0   1
  DEL PEAK  5(4Q22.1) MUTATED    12   1
  DEL PEAK  5(4Q22.1) WILD-TYPE 122  27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4Q22.1) MUTATED     12    1
  DEL PEAK  5(4Q22.1) WILD-TYPE  122   27
                    clus
vv                   DEL PEAK  5(4Q22.1) MUTATED DEL PEAK  5(4Q22.1) WILD-TYPE
  ADRENAL GLAND                               12                           122
  EXTRA-ADRENAL SITE                           1                            27
[1] 2 2
[1] FALSE
D11V4, binary
                               cls
clus                             0  1
  DEL PEAK  5(4Q22.1) MUTATED    6  7
  DEL PEAK  5(4Q22.1) WILD-TYPE 82 67
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4Q22.1) MUTATED      6    7
  DEL PEAK  5(4Q22.1) WILD-TYPE   82   67
        clus
vv       DEL PEAK  5(4Q22.1) MUTATED DEL PEAK  5(4Q22.1) WILD-TYPE
  FEMALE                           6                            82
  MALE                             7                            67
[1] 2 2
[1] FALSE
D11V5, binary
                               cls
clus                              0   1
  DEL PEAK  5(4Q22.1) MUTATED    13   0
  DEL PEAK  5(4Q22.1) WILD-TYPE 142   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4Q22.1) MUTATED     13    0
  DEL PEAK  5(4Q22.1) WILD-TYPE  142    5
     clus
vv    DEL PEAK  5(4Q22.1) MUTATED DEL PEAK  5(4Q22.1) WILD-TYPE
  NO                           13                           142
  YES                           0                             5
[1] 2 2
[1] FALSE
D11V6, continuous
                               vv
clus                            PARAGANGLIOMA
  DEL PEAK  5(4Q22.1) MUTATED               0
  DEL PEAK  5(4Q22.1) WILD-TYPE            16
                               vv
clus                            PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK  5(4Q22.1) MUTATED                                               1
  DEL PEAK  5(4Q22.1) WILD-TYPE                                            10
                               vv
clus                            PHEOCHROMOCYTOMA
  DEL PEAK  5(4Q22.1) MUTATED                 12
  DEL PEAK  5(4Q22.1) WILD-TYPE              123
D11V7, multiclass
                                               clus
vv                                              DEL PEAK  5(4Q22.1) MUTATED
  PARAGANGLIOMA                                                           0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                           1
  PHEOCHROMOCYTOMA                                                       12
                                               clus
vv                                              DEL PEAK  5(4Q22.1) 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"
D11V8, continuous
[1] "Remove cluster labels:"      "DEL PEAK  5(4Q22.1) MUTATED"
clus
  DEL PEAK  5(4Q22.1) MUTATED DEL PEAK  5(4Q22.1) WILD-TYPE 
                            1                            17 
                   TCGA-QR-A70D                    TCGA-QR-A70P 
"DEL PEAK  5(4Q22.1) WILD-TYPE" "DEL PEAK  5(4Q22.1) WILD-TYPE" 
                   TCGA-WB-A814                    TCGA-WB-A820 
"DEL PEAK  5(4Q22.1) WILD-TYPE" "DEL PEAK  5(4Q22.1) WILD-TYPE" 
                   TCGA-XG-A823                    TCGA-PR-A5PG 
"DEL PEAK  5(4Q22.1) WILD-TYPE" "DEL PEAK  5(4Q22.1) WILD-TYPE" 
                   TCGA-PR-A5PH                    TCGA-QR-A702 
"DEL PEAK  5(4Q22.1) WILD-TYPE" "DEL PEAK  5(4Q22.1) WILD-TYPE" 
                   TCGA-QT-A5XJ                    TCGA-QT-A5XP 
"DEL PEAK  5(4Q22.1) WILD-TYPE" "DEL PEAK  5(4Q22.1) WILD-TYPE" 
                   TCGA-RW-A680                    TCGA-RW-A686 
"DEL PEAK  5(4Q22.1) WILD-TYPE" "DEL PEAK  5(4Q22.1) WILD-TYPE" 
                   TCGA-RW-A8AZ                    TCGA-TT-A6YK 
"DEL PEAK  5(4Q22.1) WILD-TYPE" "DEL PEAK  5(4Q22.1) WILD-TYPE" 
                   TCGA-WB-A80Q                    TCGA-WB-A80Y 
"DEL PEAK  5(4Q22.1) WILD-TYPE" "DEL PEAK  5(4Q22.1) WILD-TYPE" 
                   TCGA-WB-A81W 
"DEL PEAK  5(4Q22.1) WILD-TYPE" 
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(4Q22.1) MUTATED                                  0     0
  DEL PEAK  5(4Q22.1) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(4Q22.1) MUTATED                           2    11
  DEL PEAK  5(4Q22.1) WILD-TYPE                        17   123
D11V9, multiclass
                                  clus
vv                                 DEL PEAK  5(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     11
                                  clus
vv                                 DEL PEAK  5(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      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(12) Variable = DEL PEAK  6(4Q34.2) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(4Q34.2) MUTATED    12   1
  DEL PEAK  6(4Q34.2) WILD-TYPE 144   5
  DEL PEAK  6(4Q34.2) MUTATED DEL PEAK  6(4Q34.2) WILD-TYPE 
                           13                           149 
  DEL PEAK  6(4Q34.2) MUTATED DEL PEAK  6(4Q34.2) WILD-TYPE 
                            1                             5 
$`DEL PEAK  6(4Q34.2) MUTATED`
TCGA-QR-A700 TCGA-QR-A6GS TCGA-QR-A70N TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RT-A6YA 
       32.15         1.25         1.41         2.30         0.79        50.63 
TCGA-RW-A67X TCGA-RW-A688 TCGA-RW-A68C TCGA-TT-A6YP TCGA-WB-A80Y TCGA-WB-A81J 
        2.93         1.22         6.28        42.48        19.59        24.36 
TCGA-WB-A821 
       93.11 

$`DEL PEAK  6(4Q34.2) 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-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-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-A689 TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
        0.85        19.30        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-W2-A7H5 
       49.61         4.34        37.35        19.92        13.32        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-A815 TCGA-WB-A816 TCGA-WB-A818 
      316.73       127.56        29.16        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-A822 
       23.77        25.51        71.05        78.21       103.17 

  DEL PEAK  6(4Q34.2) MUTATED DEL PEAK  6(4Q34.2) WILD-TYPE 
                         0.79                          0.10 
  DEL PEAK  6(4Q34.2) MUTATED DEL PEAK  6(4Q34.2) WILD-TYPE 
                        93.11                        316.73 
  DEL PEAK  6(4Q34.2) MUTATED DEL PEAK  6(4Q34.2) WILD-TYPE 
                         6.28                         25.32 
[1] "0.8 - 93.1 (6.3)"   "0.1 - 316.7 (25.3)"
[1] "hr=" "4.5"
D12V2, continuous
D12V3, binary
                               cls
clus                              0   1
  DEL PEAK  6(4Q34.2) MUTATED    13   0
  DEL PEAK  6(4Q34.2) WILD-TYPE 121  28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.2) MUTATED     13    0
  DEL PEAK  6(4Q34.2) WILD-TYPE  121   28
                    clus
vv                   DEL PEAK  6(4Q34.2) MUTATED DEL PEAK  6(4Q34.2) WILD-TYPE
  ADRENAL GLAND                               13                           121
  EXTRA-ADRENAL SITE                           0                            28
[1] 2 2
[1] FALSE
D12V4, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.2) MUTATED    7  6
  DEL PEAK  6(4Q34.2) WILD-TYPE 81 68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.2) MUTATED      7    6
  DEL PEAK  6(4Q34.2) WILD-TYPE   81   68
        clus
vv       DEL PEAK  6(4Q34.2) MUTATED DEL PEAK  6(4Q34.2) WILD-TYPE
  FEMALE                           7                            81
  MALE                             6                            68
[1] 2 2
[1] FALSE
D12V5, binary
                               cls
clus                              0   1
  DEL PEAK  6(4Q34.2) MUTATED    13   0
  DEL PEAK  6(4Q34.2) WILD-TYPE 142   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.2) MUTATED     13    0
  DEL PEAK  6(4Q34.2) WILD-TYPE  142    5
     clus
vv    DEL PEAK  6(4Q34.2) MUTATED DEL PEAK  6(4Q34.2) WILD-TYPE
  NO                           13                           142
  YES                           0                             5
[1] 2 2
[1] FALSE
D12V6, continuous
                               vv
clus                            PARAGANGLIOMA
  DEL PEAK  6(4Q34.2) MUTATED               0
  DEL PEAK  6(4Q34.2) WILD-TYPE            16
                               vv
clus                            PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK  6(4Q34.2) MUTATED                                               0
  DEL PEAK  6(4Q34.2) WILD-TYPE                                            11
                               vv
clus                            PHEOCHROMOCYTOMA
  DEL PEAK  6(4Q34.2) MUTATED                 13
  DEL PEAK  6(4Q34.2) WILD-TYPE              122
D12V7, multiclass
                                               clus
vv                                              DEL PEAK  6(4Q34.2) MUTATED
  PARAGANGLIOMA                                                           0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                           0
  PHEOCHROMOCYTOMA                                                       13
                                               clus
vv                                              DEL PEAK  6(4Q34.2) WILD-TYPE
  PARAGANGLIOMA                                                            16
  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"
D12V8, continuous
[1] "Remove cluster labels:"      "DEL PEAK  6(4Q34.2) MUTATED"
clus
  DEL PEAK  6(4Q34.2) MUTATED DEL PEAK  6(4Q34.2) WILD-TYPE 
                            2                            16 
                   TCGA-QR-A70D                    TCGA-QR-A70P 
"DEL PEAK  6(4Q34.2) WILD-TYPE" "DEL PEAK  6(4Q34.2) WILD-TYPE" 
                   TCGA-WB-A814                    TCGA-WB-A820 
"DEL PEAK  6(4Q34.2) WILD-TYPE" "DEL PEAK  6(4Q34.2) WILD-TYPE" 
                   TCGA-XG-A823                    TCGA-PR-A5PG 
"DEL PEAK  6(4Q34.2) WILD-TYPE" "DEL PEAK  6(4Q34.2) WILD-TYPE" 
                   TCGA-PR-A5PH                    TCGA-QR-A702 
"DEL PEAK  6(4Q34.2) WILD-TYPE" "DEL PEAK  6(4Q34.2) WILD-TYPE" 
                   TCGA-QT-A5XJ                    TCGA-QT-A5XP 
"DEL PEAK  6(4Q34.2) WILD-TYPE" "DEL PEAK  6(4Q34.2) WILD-TYPE" 
                   TCGA-RW-A680                    TCGA-RW-A686 
"DEL PEAK  6(4Q34.2) WILD-TYPE" "DEL PEAK  6(4Q34.2) WILD-TYPE" 
                   TCGA-RW-A8AZ                    TCGA-TT-A6YK 
"DEL PEAK  6(4Q34.2) WILD-TYPE" "DEL PEAK  6(4Q34.2) WILD-TYPE" 
                   TCGA-WB-A80Q                    TCGA-WB-A81W 
"DEL PEAK  6(4Q34.2) WILD-TYPE" "DEL PEAK  6(4Q34.2) WILD-TYPE" 
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(4Q34.2) MUTATED                                  0     0
  DEL PEAK  6(4Q34.2) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(4Q34.2) MUTATED                           2    11
  DEL PEAK  6(4Q34.2) WILD-TYPE                        17   123
D12V9, multiclass
                                  clus
vv                                 DEL PEAK  6(4Q34.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     11
                                  clus
vv                                 DEL PEAK  6(4Q34.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      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(13) Variable = DEL PEAK  7(5Q15) MUTATION ANALYSIS
D13V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  7(5Q15) MUTATED    12   0
  DEL PEAK  7(5Q15) WILD-TYPE 144   6
  DEL PEAK  7(5Q15) MUTATED DEL PEAK  7(5Q15) WILD-TYPE 
                         12                         150 
  DEL PEAK  7(5Q15) MUTATED DEL PEAK  7(5Q15) WILD-TYPE 
                          0                           6 
$`DEL PEAK  7(5Q15) MUTATED`
TCGA-P8-A6RX TCGA-QR-A7IN TCGA-QT-A5XJ TCGA-QT-A69Q TCGA-RW-A67Y TCGA-RW-A68C 
       17.75        12.39        36.23         0.79         7.10         6.28 
TCGA-SR-A6MQ TCGA-SR-A6MY TCGA-WB-A80M TCGA-WB-A81K TCGA-WB-A81S TCGA-WB-A81W 
       68.61        24.66         4.47        40.04        23.77        78.21 

$`DEL PEAK  7(5Q15) 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-A6RY TCGA-PR-A5PF TCGA-PR-A5PG 
       31.46        29.03         4.04         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-A7IP TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
        6.02        17.95         6.94         1.81         0.72        25.18 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        2.30         4.41        13.08        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A680 
       50.63         8.09        86.89        19.86         2.93        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-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-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
        1.41         0.10        51.22        81.93       106.75       110.53 
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-A80N 
       16.60        25.61        14.79        41.26        34.26         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-A81M TCGA-WB-A81N 
       38.76        63.98        22.32        24.36        45.83        62.04 
TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A821 TCGA-WB-A822 
       12.99         1.61        25.51        71.05        93.11       103.17 

  DEL PEAK  7(5Q15) MUTATED DEL PEAK  7(5Q15) WILD-TYPE 
                       0.79                        0.10 
  DEL PEAK  7(5Q15) MUTATED DEL PEAK  7(5Q15) WILD-TYPE 
                      78.21                      316.73 
  DEL PEAK  7(5Q15) MUTATED DEL PEAK  7(5Q15) WILD-TYPE 
                      20.76                       25.25 
[1] "0.8 - 78.2 (20.8)"  "0.1 - 316.7 (25.2)"
[1] "hr="     "2.7e+07"
D13V2, continuous
D13V3, binary
                             cls
clus                            0   1
  DEL PEAK  7(5Q15) MUTATED    10   2
  DEL PEAK  7(5Q15) WILD-TYPE 124  26
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(5Q15) MUTATED     10    2
  DEL PEAK  7(5Q15) WILD-TYPE  124   26
                    clus
vv                   DEL PEAK  7(5Q15) MUTATED DEL PEAK  7(5Q15) WILD-TYPE
  ADRENAL GLAND                             10                         124
  EXTRA-ADRENAL SITE                         2                          26
[1] 2 2
[1] FALSE
D13V4, binary
                             cls
clus                           0  1
  DEL PEAK  7(5Q15) MUTATED    6  6
  DEL PEAK  7(5Q15) WILD-TYPE 82 68
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(5Q15) MUTATED      6    6
  DEL PEAK  7(5Q15) WILD-TYPE   82   68
        clus
vv       DEL PEAK  7(5Q15) MUTATED DEL PEAK  7(5Q15) WILD-TYPE
  FEMALE                         6                          82
  MALE                           6                          68
[1] 2 2
[1] FALSE
D13V5, binary
                             cls
clus                            0   1
  DEL PEAK  7(5Q15) MUTATED    12   0
  DEL PEAK  7(5Q15) WILD-TYPE 143   5
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(5Q15) MUTATED     12    0
  DEL PEAK  7(5Q15) WILD-TYPE  143    5
     clus
vv    DEL PEAK  7(5Q15) MUTATED DEL PEAK  7(5Q15) WILD-TYPE
  NO                         12                         143
  YES                         0                           5
[1] 2 2
[1] FALSE
D13V6, continuous
                             vv
clus                          PARAGANGLIOMA
  DEL PEAK  7(5Q15) MUTATED               2
  DEL PEAK  7(5Q15) WILD-TYPE            14
                             vv
clus                          PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK  7(5Q15) MUTATED                                               0
  DEL PEAK  7(5Q15) WILD-TYPE                                            11
                             vv
clus                          PHEOCHROMOCYTOMA
  DEL PEAK  7(5Q15) MUTATED                 10
  DEL PEAK  7(5Q15) WILD-TYPE              125
D13V7, multiclass
                                               clus
vv                                              DEL PEAK  7(5Q15) MUTATED
  PARAGANGLIOMA                                                         2
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                         0
  PHEOCHROMOCYTOMA                                                     10
                                               clus
vv                                              DEL PEAK  7(5Q15) 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"
D13V8, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(5Q15) MUTATED                                  0     1
  DEL PEAK  7(5Q15) WILD-TYPE                                1     4
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(5Q15) MUTATED                           2     9
  DEL PEAK  7(5Q15) WILD-TYPE                        17   125
D13V9, multiclass
                                  clus
vv                                 DEL PEAK  7(5Q15) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                    9
                                  clus
vv                                 DEL PEAK  7(5Q15) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                    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(14) Variable = DEL PEAK  8(6P12.3) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(6P12.3) MUTATED    10   0
  DEL PEAK  8(6P12.3) WILD-TYPE 146   6
  DEL PEAK  8(6P12.3) MUTATED DEL PEAK  8(6P12.3) WILD-TYPE 
                           10                           152 
  DEL PEAK  8(6P12.3) MUTATED DEL PEAK  8(6P12.3) WILD-TYPE 
                            0                             6 
$`DEL PEAK  8(6P12.3) MUTATED`
TCGA-QR-A700 TCGA-SR-A6MV TCGA-XG-A823 TCGA-QR-A706 TCGA-QR-A70R TCGA-QR-A70X 
       32.15       121.05        20.19         4.11        14.20         6.02 
TCGA-SR-A6MU TCGA-TT-A6YJ TCGA-TT-A6YO TCGA-WB-A81S 
      110.53         4.34        13.32        23.77 

$`DEL PEAK  8(6P12.3) 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-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-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-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-A70C 
        9.93        14.27        31.53        15.58         1.28       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-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK 
        1.41        41.79        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-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-A6MT 
        1.41         0.10        51.22        68.61        81.93       106.75 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YP 
       24.66        26.20        49.61        37.35        19.92        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-A81T TCGA-WB-A81V TCGA-WB-A81W 
       62.04        12.99         1.61        25.51        71.05        78.21 
TCGA-WB-A821 TCGA-WB-A822 
       93.11       103.17 

  DEL PEAK  8(6P12.3) MUTATED DEL PEAK  8(6P12.3) WILD-TYPE 
                         4.11                          0.10 
  DEL PEAK  8(6P12.3) MUTATED DEL PEAK  8(6P12.3) WILD-TYPE 
                       121.05                        316.73 
  DEL PEAK  8(6P12.3) MUTATED DEL PEAK  8(6P12.3) WILD-TYPE 
                       17.195                        25.250 
[1] "4.1 - 121.0 (17.2)" "0.1 - 316.7 (25.2)"
[1] "hr="     "8.1e+07"
D14V2, continuous
D14V3, binary
                               cls
clus                              0   1
  DEL PEAK  8(6P12.3) MUTATED     8   2
  DEL PEAK  8(6P12.3) WILD-TYPE 126  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(6P12.3) MUTATED      8    2
  DEL PEAK  8(6P12.3) WILD-TYPE  126   26
                    clus
vv                   DEL PEAK  8(6P12.3) MUTATED DEL PEAK  8(6P12.3) WILD-TYPE
  ADRENAL GLAND                                8                           126
  EXTRA-ADRENAL SITE                           2                            26
[1] 2 2
[1] FALSE
D14V4, binary
                               cls
clus                             0  1
  DEL PEAK  8(6P12.3) MUTATED    8  2
  DEL PEAK  8(6P12.3) WILD-TYPE 80 72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(6P12.3) MUTATED      8    2
  DEL PEAK  8(6P12.3) WILD-TYPE   80   72
        clus
vv       DEL PEAK  8(6P12.3) MUTATED DEL PEAK  8(6P12.3) WILD-TYPE
  FEMALE                           8                            80
  MALE                             2                            72
[1] 2 2
[1] FALSE
D14V5, binary
                               cls
clus                              0   1
  DEL PEAK  8(6P12.3) MUTATED     9   1
  DEL PEAK  8(6P12.3) WILD-TYPE 146   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(6P12.3) MUTATED      9    1
  DEL PEAK  8(6P12.3) WILD-TYPE  146    4
     clus
vv    DEL PEAK  8(6P12.3) MUTATED DEL PEAK  8(6P12.3) WILD-TYPE
  NO                            9                           146
  YES                           1                             4
[1] 2 2
[1] FALSE
D14V6, continuous
                               vv
clus                            PARAGANGLIOMA
  DEL PEAK  8(6P12.3) MUTATED               2
  DEL PEAK  8(6P12.3) WILD-TYPE            14
                               vv
clus                            PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK  8(6P12.3) MUTATED                                               0
  DEL PEAK  8(6P12.3) WILD-TYPE                                            11
                               vv
clus                            PHEOCHROMOCYTOMA
  DEL PEAK  8(6P12.3) MUTATED                  8
  DEL PEAK  8(6P12.3) WILD-TYPE              127
D14V7, multiclass
                                               clus
vv                                              DEL PEAK  8(6P12.3) MUTATED
  PARAGANGLIOMA                                                           2
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                           0
  PHEOCHROMOCYTOMA                                                        8
                                               clus
vv                                              DEL PEAK  8(6P12.3) WILD-TYPE
  PARAGANGLIOMA                                                            14
  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"
D14V8, continuous
[1] "Remove cluster labels:"      "DEL PEAK  8(6P12.3) MUTATED"
clus
  DEL PEAK  8(6P12.3) MUTATED DEL PEAK  8(6P12.3) WILD-TYPE 
                            1                            17 
                   TCGA-QR-A70D                    TCGA-QR-A70P 
"DEL PEAK  8(6P12.3) WILD-TYPE" "DEL PEAK  8(6P12.3) WILD-TYPE" 
                   TCGA-WB-A814                    TCGA-WB-A820 
"DEL PEAK  8(6P12.3) WILD-TYPE" "DEL PEAK  8(6P12.3) WILD-TYPE" 
                   TCGA-PR-A5PG                    TCGA-PR-A5PH 
"DEL PEAK  8(6P12.3) WILD-TYPE" "DEL PEAK  8(6P12.3) WILD-TYPE" 
                   TCGA-QR-A702                    TCGA-QT-A5XJ 
"DEL PEAK  8(6P12.3) WILD-TYPE" "DEL PEAK  8(6P12.3) WILD-TYPE" 
                   TCGA-QT-A5XP                    TCGA-QT-A69Q 
"DEL PEAK  8(6P12.3) WILD-TYPE" "DEL PEAK  8(6P12.3) WILD-TYPE" 
                   TCGA-RW-A680                    TCGA-RW-A686 
"DEL PEAK  8(6P12.3) WILD-TYPE" "DEL PEAK  8(6P12.3) WILD-TYPE" 
                   TCGA-RW-A8AZ                    TCGA-TT-A6YK 
"DEL PEAK  8(6P12.3) WILD-TYPE" "DEL PEAK  8(6P12.3) WILD-TYPE" 
                   TCGA-WB-A80Q                    TCGA-WB-A80Y 
"DEL PEAK  8(6P12.3) WILD-TYPE" "DEL PEAK  8(6P12.3) WILD-TYPE" 
                   TCGA-WB-A81W 
"DEL PEAK  8(6P12.3) WILD-TYPE" 
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(6P12.3) MUTATED                                  0     0
  DEL PEAK  8(6P12.3) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(6P12.3) MUTATED                           2     7
  DEL PEAK  8(6P12.3) WILD-TYPE                        17   127
D14V9, multiclass
                                  clus
vv                                 DEL PEAK  8(6P12.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                      7
                                  clus
vv                                 DEL PEAK  8(6P12.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      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(15) Variable = DEL PEAK  9(6Q16.1) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(6Q16.1) MUTATED    23   1
  DEL PEAK  9(6Q16.1) WILD-TYPE 133   5
  DEL PEAK  9(6Q16.1) MUTATED DEL PEAK  9(6Q16.1) WILD-TYPE 
                           24                           138 
  DEL PEAK  9(6Q16.1) MUTATED DEL PEAK  9(6Q16.1) WILD-TYPE 
                            1                             5 
$`DEL PEAK  9(6Q16.1) MUTATED`
TCGA-QR-A700 TCGA-SR-A6MV TCGA-WB-A820 TCGA-XG-A823 TCGA-P8-A5KD TCGA-QR-A6GO 
       32.15       121.05        10.16        20.19         4.04        35.01 
TCGA-QR-A706 TCGA-QR-A70W TCGA-QR-A70X TCGA-QT-A5XN TCGA-S7-A7WM TCGA-S7-A7WN 
        4.11        41.79         6.02        25.18        36.56        37.25 
TCGA-S7-A7WR TCGA-SR-A6MU TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-TT-A6YO TCGA-W2-A7HC 
       40.70       110.53        24.66         4.34        13.32        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 

$`DEL PEAK  9(6Q16.1) 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-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-A81Q TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY 
       48.53        24.82        31.46        29.03        17.75         5.88 
TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       17.95        81.70        28.08        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-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
       15.58         1.28       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-A7IN 
       29.92        13.12         9.01         1.41        14.20        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-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-A7WO TCGA-S7-A7WP TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW 
       31.59        35.51        31.04        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-A6MZ 
        0.10        51.22        68.61        81.93       106.75        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       49.61        37.35        19.92        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 

  DEL PEAK  9(6Q16.1) MUTATED DEL PEAK  9(6Q16.1) WILD-TYPE 
                         1.61                          0.10 
  DEL PEAK  9(6Q16.1) MUTATED DEL PEAK  9(6Q16.1) WILD-TYPE 
                       121.05                        316.73 
  DEL PEAK  9(6Q16.1) MUTATED DEL PEAK  9(6Q16.1) WILD-TYPE 
                       24.920                        24.935 
[1] "1.6 - 121.0 (24.9)" "0.1 - 316.7 (24.9)"
[1] "hr=" "1"  
D15V2, continuous
D15V3, binary
                               cls
clus                              0   1
  DEL PEAK  9(6Q16.1) MUTATED    22   2
  DEL PEAK  9(6Q16.1) WILD-TYPE 112  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6Q16.1) MUTATED     22    2
  DEL PEAK  9(6Q16.1) WILD-TYPE  112   26
                    clus
vv                   DEL PEAK  9(6Q16.1) MUTATED DEL PEAK  9(6Q16.1) WILD-TYPE
  ADRENAL GLAND                               22                           112
  EXTRA-ADRENAL SITE                           2                            26
[1] 2 2
[1] FALSE
D15V4, binary
                               cls
clus                             0  1
  DEL PEAK  9(6Q16.1) MUTATED   16  8
  DEL PEAK  9(6Q16.1) WILD-TYPE 72 66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6Q16.1) MUTATED     16    8
  DEL PEAK  9(6Q16.1) WILD-TYPE   72   66
        clus
vv       DEL PEAK  9(6Q16.1) MUTATED DEL PEAK  9(6Q16.1) WILD-TYPE
  FEMALE                          16                            72
  MALE                             8                            66
[1] 2 2
[1] FALSE
D15V5, binary
                               cls
clus                              0   1
  DEL PEAK  9(6Q16.1) MUTATED    23   1
  DEL PEAK  9(6Q16.1) WILD-TYPE 132   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6Q16.1) MUTATED     23    1
  DEL PEAK  9(6Q16.1) WILD-TYPE  132    4
     clus
vv    DEL PEAK  9(6Q16.1) MUTATED DEL PEAK  9(6Q16.1) WILD-TYPE
  NO                           23                           132
  YES                           1                             4
[1] 2 2
[1] FALSE
D15V6, continuous
                               vv
clus                            PARAGANGLIOMA
  DEL PEAK  9(6Q16.1) MUTATED               2
  DEL PEAK  9(6Q16.1) WILD-TYPE            14
                               vv
clus                            PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK  9(6Q16.1) MUTATED                                               0
  DEL PEAK  9(6Q16.1) WILD-TYPE                                            11
                               vv
clus                            PHEOCHROMOCYTOMA
  DEL PEAK  9(6Q16.1) MUTATED                 22
  DEL PEAK  9(6Q16.1) WILD-TYPE              113
D15V7, multiclass
                                               clus
vv                                              DEL PEAK  9(6Q16.1) MUTATED
  PARAGANGLIOMA                                                           2
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                           0
  PHEOCHROMOCYTOMA                                                       22
                                               clus
vv                                              DEL PEAK  9(6Q16.1) WILD-TYPE
  PARAGANGLIOMA                                                            14
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                            11
  PHEOCHROMOCYTOMA                                                        113
[1] 3 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
[1] "Remove cluster labels:"      "DEL PEAK  9(6Q16.1) MUTATED"
clus
  DEL PEAK  9(6Q16.1) MUTATED DEL PEAK  9(6Q16.1) WILD-TYPE 
                            2                            16 
                   TCGA-QR-A70D                    TCGA-QR-A70P 
"DEL PEAK  9(6Q16.1) WILD-TYPE" "DEL PEAK  9(6Q16.1) WILD-TYPE" 
                   TCGA-WB-A814                    TCGA-PR-A5PG 
"DEL PEAK  9(6Q16.1) WILD-TYPE" "DEL PEAK  9(6Q16.1) WILD-TYPE" 
                   TCGA-PR-A5PH                    TCGA-QR-A702 
"DEL PEAK  9(6Q16.1) WILD-TYPE" "DEL PEAK  9(6Q16.1) WILD-TYPE" 
                   TCGA-QT-A5XJ                    TCGA-QT-A5XP 
"DEL PEAK  9(6Q16.1) WILD-TYPE" "DEL PEAK  9(6Q16.1) WILD-TYPE" 
                   TCGA-QT-A69Q                    TCGA-RW-A680 
"DEL PEAK  9(6Q16.1) WILD-TYPE" "DEL PEAK  9(6Q16.1) WILD-TYPE" 
                   TCGA-RW-A686                    TCGA-RW-A8AZ 
"DEL PEAK  9(6Q16.1) WILD-TYPE" "DEL PEAK  9(6Q16.1) WILD-TYPE" 
                   TCGA-TT-A6YK                    TCGA-WB-A80Q 
"DEL PEAK  9(6Q16.1) WILD-TYPE" "DEL PEAK  9(6Q16.1) WILD-TYPE" 
                   TCGA-WB-A80Y                    TCGA-WB-A81W 
"DEL PEAK  9(6Q16.1) WILD-TYPE" "DEL PEAK  9(6Q16.1) WILD-TYPE" 
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(6Q16.1) MUTATED                                  0     0
  DEL PEAK  9(6Q16.1) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(6Q16.1) MUTATED                           3    20
  DEL PEAK  9(6Q16.1) WILD-TYPE                        16   114
D15V9, multiclass
                                  clus
vv                                 DEL PEAK  9(6Q16.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     20
                                  clus
vv                                 DEL PEAK  9(6Q16.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                      114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = DEL PEAK 10(8P22) MUTATION ANALYSIS
D16V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 10(8P22) MUTATED    23   2
  DEL PEAK 10(8P22) WILD-TYPE 133   4
  DEL PEAK 10(8P22) MUTATED DEL PEAK 10(8P22) WILD-TYPE 
                         25                         137 
  DEL PEAK 10(8P22) MUTATED DEL PEAK 10(8P22) WILD-TYPE 
                          2                           4 
$`DEL PEAK 10(8P22) 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-A7WL TCGA-S7-A7WR TCGA-S7-A7WT TCGA-SP-A6QI TCGA-SR-A6MP TCGA-SR-A6MT 
       31.59        40.70        42.77       110.04        51.22       106.75 
TCGA-W2-A7H5 TCGA-W2-A7HE TCGA-WB-A80V TCGA-WB-A81D TCGA-WB-A81P TCGA-WB-A81R 
       20.09        16.60        29.16        35.84        12.99         1.61 
TCGA-WB-A81T 
       25.51 

$`DEL PEAK 10(8P22) 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-A7WM TCGA-S7-A7WN 
        6.28        11.57         2.89        20.09        36.56        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       35.51        31.04        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-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MS 
       15.52       111.25         1.41         0.10        68.61        81.93 
TCGA-SR-A6MU TCGA-SR-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-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC 
       19.92        13.32        42.48        17.16         1.18        14.43 
TCGA-W2-A7HD TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       18.44        25.61        14.79        41.26        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A815 
        4.73        25.51       316.73       127.56        19.59        53.59 
TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81F TCGA-WB-A81G 
       41.23        42.35        33.90        24.16        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-A81S TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       23.77        71.05        78.21        93.11       103.17 

  DEL PEAK 10(8P22) MUTATED DEL PEAK 10(8P22) WILD-TYPE 
                       1.61                        0.10 
  DEL PEAK 10(8P22) MUTATED DEL PEAK 10(8P22) WILD-TYPE 
                     137.59                      316.73 
  DEL PEAK 10(8P22) MUTATED DEL PEAK 10(8P22) WILD-TYPE 
                      29.16                       24.16 
[1] "1.6 - 137.6 (29.2)" "0.1 - 316.7 (24.2)"
[1] "hr=" "2.2"
D16V2, continuous
D16V3, binary
                             cls
clus                            0   1
  DEL PEAK 10(8P22) MUTATED    24   1
  DEL PEAK 10(8P22) WILD-TYPE 110  27
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(8P22) MUTATED     24    1
  DEL PEAK 10(8P22) WILD-TYPE  110   27
                    clus
vv                   DEL PEAK 10(8P22) MUTATED DEL PEAK 10(8P22) WILD-TYPE
  ADRENAL GLAND                             24                         110
  EXTRA-ADRENAL SITE                         1                          27
[1] 2 2
[1] FALSE
D16V4, binary
                             cls
clus                           0  1
  DEL PEAK 10(8P22) MUTATED   16  9
  DEL PEAK 10(8P22) WILD-TYPE 72 65
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(8P22) MUTATED     16    9
  DEL PEAK 10(8P22) WILD-TYPE   72   65
        clus
vv       DEL PEAK 10(8P22) MUTATED DEL PEAK 10(8P22) WILD-TYPE
  FEMALE                        16                          72
  MALE                           9                          65
[1] 2 2
[1] FALSE
D16V5, binary
                             cls
clus                            0   1
  DEL PEAK 10(8P22) MUTATED    24   1
  DEL PEAK 10(8P22) WILD-TYPE 131   4
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(8P22) MUTATED     24    1
  DEL PEAK 10(8P22) WILD-TYPE  131    4
     clus
vv    DEL PEAK 10(8P22) MUTATED DEL PEAK 10(8P22) WILD-TYPE
  NO                         24                         131
  YES                         1                           4
[1] 2 2
[1] FALSE
D16V6, continuous
                             vv
clus                          PARAGANGLIOMA
  DEL PEAK 10(8P22) MUTATED               0
  DEL PEAK 10(8P22) WILD-TYPE            16
                             vv
clus                          PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK 10(8P22) MUTATED                                               0
  DEL PEAK 10(8P22) WILD-TYPE                                            11
                             vv
clus                          PHEOCHROMOCYTOMA
  DEL PEAK 10(8P22) MUTATED                 25
  DEL PEAK 10(8P22) WILD-TYPE              110
D16V7, multiclass
                                               clus
vv                                              DEL PEAK 10(8P22) MUTATED
  PARAGANGLIOMA                                                         0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                         0
  PHEOCHROMOCYTOMA                                                     25
                                               clus
vv                                              DEL PEAK 10(8P22) WILD-TYPE
  PARAGANGLIOMA                                                          16
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                          11
  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"
D16V8, continuous
[1] "Remove cluster labels:"    "DEL PEAK 10(8P22) MUTATED"
clus
  DEL PEAK 10(8P22) MUTATED DEL PEAK 10(8P22) WILD-TYPE 
                          2                          16 
                 TCGA-QR-A70D                  TCGA-QR-A70P 
"DEL PEAK 10(8P22) WILD-TYPE" "DEL PEAK 10(8P22) WILD-TYPE" 
                 TCGA-WB-A814                  TCGA-XG-A823 
"DEL PEAK 10(8P22) WILD-TYPE" "DEL PEAK 10(8P22) WILD-TYPE" 
                 TCGA-PR-A5PH                  TCGA-QR-A702 
"DEL PEAK 10(8P22) WILD-TYPE" "DEL PEAK 10(8P22) WILD-TYPE" 
                 TCGA-QT-A5XJ                  TCGA-QT-A5XP 
"DEL PEAK 10(8P22) WILD-TYPE" "DEL PEAK 10(8P22) WILD-TYPE" 
                 TCGA-QT-A69Q                  TCGA-RW-A680 
"DEL PEAK 10(8P22) WILD-TYPE" "DEL PEAK 10(8P22) WILD-TYPE" 
                 TCGA-RW-A686                  TCGA-RW-A8AZ 
"DEL PEAK 10(8P22) WILD-TYPE" "DEL PEAK 10(8P22) WILD-TYPE" 
                 TCGA-TT-A6YK                  TCGA-WB-A80Q 
"DEL PEAK 10(8P22) WILD-TYPE" "DEL PEAK 10(8P22) WILD-TYPE" 
                 TCGA-WB-A80Y                  TCGA-WB-A81W 
"DEL PEAK 10(8P22) WILD-TYPE" "DEL PEAK 10(8P22) WILD-TYPE" 
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(8P22) MUTATED                                  0     1
  DEL PEAK 10(8P22) WILD-TYPE                                1     4
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(8P22) MUTATED                           2    22
  DEL PEAK 10(8P22) WILD-TYPE                        17   112
D16V9, multiclass
                                  clus
vv                                 DEL PEAK 10(8P22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                   22
                                  clus
vv                                 DEL PEAK 10(8P22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                    112
[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 = DEL PEAK 11(8Q23.3) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(8Q23.3) MUTATED    12   1
  DEL PEAK 11(8Q23.3) WILD-TYPE 144   5
  DEL PEAK 11(8Q23.3) MUTATED DEL PEAK 11(8Q23.3) WILD-TYPE 
                           13                           149 
  DEL PEAK 11(8Q23.3) MUTATED DEL PEAK 11(8Q23.3) WILD-TYPE 
                            1                             5 
$`DEL PEAK 11(8Q23.3) MUTATED`
TCGA-QR-A700 TCGA-RW-A68A TCGA-SR-A6MX TCGA-QR-A6GX TCGA-QR-A70K TCGA-RW-A67W 
       32.15        25.05         3.12        19.04         9.01        19.86 
TCGA-S7-A7WR TCGA-SR-A6MT TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HD TCGA-WB-A80K 
       40.70       106.75        20.09        17.16        18.44        41.26 
TCGA-WB-A80V 
       29.16 

$`DEL PEAK 11(8Q23.3) 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-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 
        8.09        86.89         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-A7WT TCGA-S7-A7WV TCGA-S7-A7WW 
       37.25        35.51        31.04        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-A7HA TCGA-W2-A7HC TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY 
       42.48         1.18        14.43        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-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 

  DEL PEAK 11(8Q23.3) MUTATED DEL PEAK 11(8Q23.3) WILD-TYPE 
                         3.12                          0.10 
  DEL PEAK 11(8Q23.3) MUTATED DEL PEAK 11(8Q23.3) WILD-TYPE 
                       106.75                        316.73 
  DEL PEAK 11(8Q23.3) MUTATED DEL PEAK 11(8Q23.3) WILD-TYPE 
                        20.09                         25.18 
[1] "3.1 - 106.8 (20.1)" "0.1 - 316.7 (25.2)"
[1] "hr=" "2.7"
D17V2, continuous
D17V3, binary
                               cls
clus                              0   1
  DEL PEAK 11(8Q23.3) MUTATED    12   1
  DEL PEAK 11(8Q23.3) WILD-TYPE 122  27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8Q23.3) MUTATED     12    1
  DEL PEAK 11(8Q23.3) WILD-TYPE  122   27
                    clus
vv                   DEL PEAK 11(8Q23.3) MUTATED DEL PEAK 11(8Q23.3) WILD-TYPE
  ADRENAL GLAND                               12                           122
  EXTRA-ADRENAL SITE                           1                            27
[1] 2 2
[1] FALSE
D17V4, binary
                               cls
clus                             0  1
  DEL PEAK 11(8Q23.3) MUTATED    8  5
  DEL PEAK 11(8Q23.3) WILD-TYPE 80 69
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8Q23.3) MUTATED      8    5
  DEL PEAK 11(8Q23.3) WILD-TYPE   80   69
        clus
vv       DEL PEAK 11(8Q23.3) MUTATED DEL PEAK 11(8Q23.3) WILD-TYPE
  FEMALE                           8                            80
  MALE                             5                            69
[1] 2 2
[1] FALSE
D17V5, binary
                               cls
clus                              0   1
  DEL PEAK 11(8Q23.3) MUTATED    13   0
  DEL PEAK 11(8Q23.3) WILD-TYPE 142   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(8Q23.3) MUTATED     13    0
  DEL PEAK 11(8Q23.3) WILD-TYPE  142    5
     clus
vv    DEL PEAK 11(8Q23.3) MUTATED DEL PEAK 11(8Q23.3) WILD-TYPE
  NO                           13                           142
  YES                           0                             5
[1] 2 2
[1] FALSE
D17V6, continuous
[1] "Remove cluster labels:"      "DEL PEAK 11(8Q23.3) MUTATED"
clus
  DEL PEAK 11(8Q23.3) MUTATED DEL PEAK 11(8Q23.3) WILD-TYPE 
                            2                            58 
                   TCGA-S7-A7WQ                    TCGA-S7-A7WU 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-S7-A7X1                    TCGA-SR-A6MV 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-WB-A817                    TCGA-WB-A81E 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-XG-A823                    TCGA-P7-A5NY 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-PR-A5PF                    TCGA-PR-A5PG 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-PR-A5PH                    TCGA-RT-A6YA 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-RT-A6YC                    TCGA-RX-A8JQ 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-S7-A7WL                    TCGA-S7-A7WM 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-S7-A7WN                    TCGA-S7-A7WO 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-S7-A7WP                    TCGA-S7-A7WT 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-S7-A7WV                    TCGA-S7-A7WW 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-S7-A7WX                    TCGA-S7-A7X0 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-S7-A7X2                    TCGA-SP-A6QC 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-SP-A6QD                    TCGA-SP-A6QF 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-SP-A6QG                    TCGA-SP-A6QI 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-SP-A6QJ                    TCGA-SP-A6QK 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-SR-A6MQ                    TCGA-SR-A6MS 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-SR-A6MY                    TCGA-SR-A6MZ 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-SR-A6N0                    TCGA-TT-A6YK 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-TT-A6YN                    TCGA-TT-A6YO 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-TT-A6YP                    TCGA-WB-A80L 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-WB-A80Q                    TCGA-WB-A815 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-WB-A818                    TCGA-WB-A81D 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-WB-A81F                    TCGA-WB-A81G 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-WB-A81H                    TCGA-WB-A81I 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-WB-A81J                    TCGA-WB-A81K 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-WB-A81M                    TCGA-WB-A81N 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-WB-A81S                    TCGA-WB-A81T 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                   TCGA-WB-A821                    TCGA-WB-A822 
"DEL PEAK 11(8Q23.3) WILD-TYPE" "DEL PEAK 11(8Q23.3) WILD-TYPE" 
                               vv
clus                            PARAGANGLIOMA
  DEL PEAK 11(8Q23.3) MUTATED               1
  DEL PEAK 11(8Q23.3) WILD-TYPE            15
                               vv
clus                            PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK 11(8Q23.3) MUTATED                                               0
  DEL PEAK 11(8Q23.3) WILD-TYPE                                            11
                               vv
clus                            PHEOCHROMOCYTOMA
  DEL PEAK 11(8Q23.3) MUTATED                 12
  DEL PEAK 11(8Q23.3) WILD-TYPE              123
D17V7, multiclass
                                               clus
vv                                              DEL PEAK 11(8Q23.3) MUTATED
  PARAGANGLIOMA                                                           1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                           0
  PHEOCHROMOCYTOMA                                                       12
                                               clus
vv                                              DEL PEAK 11(8Q23.3) WILD-TYPE
  PARAGANGLIOMA                                                            15
  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"
D17V8, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(8Q23.3) MUTATED                                  0     0
  DEL PEAK 11(8Q23.3) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(8Q23.3) MUTATED                           1    12
  DEL PEAK 11(8Q23.3) WILD-TYPE                        18   122
D17V9, multiclass
                                  clus
vv                                 DEL PEAK 11(8Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     12
                                  clus
vv                                 DEL PEAK 11(8Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   18
  WHITE                                                      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(18) Variable = DEL PEAK 12(9P24.2) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(9P24.2) MUTATED    12   3
  DEL PEAK 12(9P24.2) WILD-TYPE 144   3
  DEL PEAK 12(9P24.2) MUTATED DEL PEAK 12(9P24.2) WILD-TYPE 
                           15                           147 
  DEL PEAK 12(9P24.2) MUTATED DEL PEAK 12(9P24.2) WILD-TYPE 
                            3                             3 
$`DEL PEAK 12(9P24.2) MUTATED`
TCGA-SR-A6MV TCGA-WB-A81Q TCGA-WB-A820 TCGA-QR-A6GO TCGA-QR-A70H TCGA-QR-A70R 
      121.05        24.82        10.16        35.01        26.83        14.20 
TCGA-QR-A7IP TCGA-QT-A5XP TCGA-RT-A6YA TCGA-RW-A686 TCGA-RW-A8AZ TCGA-SP-A6QJ 
       17.95         4.41        50.63        19.30         2.89        15.52 
TCGA-W2-A7H5 TCGA-WB-A81J TCGA-WB-A81R 
       20.09        24.36         1.61 

$`DEL PEAK 12(9P24.2) 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-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-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-A688 
        7.10        47.64        37.51         1.05         0.85         1.22 
TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RX-A8JQ TCGA-S7-A7WL 
       27.22         6.28        72.79        11.57        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-A6QK 
      114.77       109.25        82.62        79.46       110.04       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-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC 
       19.92        13.32        42.48        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-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-A81K 
       35.84        57.11        38.76        63.98        22.32        40.04 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       45.83        62.04        12.99        23.77        25.51        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       78.21        93.11       103.17 

  DEL PEAK 12(9P24.2) MUTATED DEL PEAK 12(9P24.2) WILD-TYPE 
                         1.61                          0.10 
  DEL PEAK 12(9P24.2) MUTATED DEL PEAK 12(9P24.2) WILD-TYPE 
                       121.05                        316.73 
  DEL PEAK 12(9P24.2) MUTATED DEL PEAK 12(9P24.2) WILD-TYPE 
                        19.30                         25.51 
[1] "1.6 - 121.0 (19.3)" "0.1 - 316.7 (25.5)"
[1] "hr=" "9.5"
D18V2, continuous
D18V3, binary
                               cls
clus                              0   1
  DEL PEAK 12(9P24.2) MUTATED    13   2
  DEL PEAK 12(9P24.2) WILD-TYPE 121  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P24.2) MUTATED     13    2
  DEL PEAK 12(9P24.2) WILD-TYPE  121   26
                    clus
vv                   DEL PEAK 12(9P24.2) MUTATED DEL PEAK 12(9P24.2) WILD-TYPE
  ADRENAL GLAND                               13                           121
  EXTRA-ADRENAL SITE                           2                            26
[1] 2 2
[1] FALSE
D18V4, binary
                               cls
clus                             0  1
  DEL PEAK 12(9P24.2) MUTATED    6  9
  DEL PEAK 12(9P24.2) WILD-TYPE 82 65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P24.2) MUTATED      6    9
  DEL PEAK 12(9P24.2) WILD-TYPE   82   65
        clus
vv       DEL PEAK 12(9P24.2) MUTATED DEL PEAK 12(9P24.2) WILD-TYPE
  FEMALE                           6                            82
  MALE                             9                            65
[1] 2 2
[1] FALSE
D18V5, binary
                               cls
clus                              0   1
  DEL PEAK 12(9P24.2) MUTATED    13   2
  DEL PEAK 12(9P24.2) WILD-TYPE 142   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P24.2) MUTATED     13    2
  DEL PEAK 12(9P24.2) WILD-TYPE  142    3
     clus
vv    DEL PEAK 12(9P24.2) MUTATED DEL PEAK 12(9P24.2) WILD-TYPE
  NO                           13                           142
  YES                           2                             3
[1] 2 2
[1] FALSE
D18V6, continuous
                               vv
clus                            PARAGANGLIOMA
  DEL PEAK 12(9P24.2) MUTATED               2
  DEL PEAK 12(9P24.2) WILD-TYPE            14
                               vv
clus                            PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK 12(9P24.2) MUTATED                                               0
  DEL PEAK 12(9P24.2) WILD-TYPE                                            11
                               vv
clus                            PHEOCHROMOCYTOMA
  DEL PEAK 12(9P24.2) MUTATED                 13
  DEL PEAK 12(9P24.2) WILD-TYPE              122
D18V7, multiclass
                                               clus
vv                                              DEL PEAK 12(9P24.2) MUTATED
  PARAGANGLIOMA                                                           2
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                           0
  PHEOCHROMOCYTOMA                                                       13
                                               clus
vv                                              DEL PEAK 12(9P24.2) WILD-TYPE
  PARAGANGLIOMA                                                            14
  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"
D18V8, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(9P24.2) MUTATED                                  0     0
  DEL PEAK 12(9P24.2) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(9P24.2) MUTATED                           1    14
  DEL PEAK 12(9P24.2) WILD-TYPE                        18   120
D18V9, multiclass
                                  clus
vv                                 DEL PEAK 12(9P24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     14
                                  clus
vv                                 DEL PEAK 12(9P24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   18
  WHITE                                                      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(19) Variable = DEL PEAK 13(9Q21.12) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 13(9Q21.12) MUTATED    13   1
  DEL PEAK 13(9Q21.12) WILD-TYPE 143   5
  DEL PEAK 13(9Q21.12) MUTATED DEL PEAK 13(9Q21.12) WILD-TYPE 
                            14                            148 
  DEL PEAK 13(9Q21.12) MUTATED DEL PEAK 13(9Q21.12) WILD-TYPE 
                             1                              5 
$`DEL PEAK 13(9Q21.12) MUTATED`
TCGA-SR-A6MV TCGA-WB-A81Q TCGA-QR-A6GO TCGA-QR-A6GY TCGA-QR-A70R TCGA-QR-A7IP 
      121.05        24.82        35.01         1.05        14.20        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XP TCGA-RT-A6YA TCGA-S7-A7WL TCGA-SP-A6QJ TCGA-SR-A6MP 
       36.23         4.41        50.63        31.59        15.52        51.22 
TCGA-W2-A7H5 TCGA-W2-A7H7 
       20.09        17.16 

$`DEL PEAK 13(9Q21.12) 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-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-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6H0 TCGA-QR-A6H2 
       23.11         1.25       137.59        19.04         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-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-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-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-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-A7HA TCGA-W2-A7HC TCGA-W2-A7HD 
       19.92        13.32        42.48         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 

  DEL PEAK 13(9Q21.12) MUTATED DEL PEAK 13(9Q21.12) WILD-TYPE 
                          1.05                           0.10 
  DEL PEAK 13(9Q21.12) MUTATED DEL PEAK 13(9Q21.12) WILD-TYPE 
                        121.05                         316.73 
  DEL PEAK 13(9Q21.12) MUTATED DEL PEAK 13(9Q21.12) WILD-TYPE 
                        22.455                         25.115 
[1] "1.1 - 121.0 (22.5)" "0.1 - 316.7 (25.1)"
[1] "hr=" "1.7"
D19V2, continuous
D19V3, binary
                                cls
clus                               0   1
  DEL PEAK 13(9Q21.12) MUTATED    12   2
  DEL PEAK 13(9Q21.12) WILD-TYPE 122  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(9Q21.12) MUTATED     12    2
  DEL PEAK 13(9Q21.12) WILD-TYPE  122   26
                    clus
vv                   DEL PEAK 13(9Q21.12) MUTATED
  ADRENAL GLAND                                12
  EXTRA-ADRENAL SITE                            2
                    clus
vv                   DEL PEAK 13(9Q21.12) WILD-TYPE
  ADRENAL GLAND                                 122
  EXTRA-ADRENAL SITE                             26
[1] 2 2
[1] FALSE
D19V4, binary
                                cls
clus                              0  1
  DEL PEAK 13(9Q21.12) MUTATED    8  6
  DEL PEAK 13(9Q21.12) WILD-TYPE 80 68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(9Q21.12) MUTATED      8    6
  DEL PEAK 13(9Q21.12) WILD-TYPE   80   68
        clus
vv       DEL PEAK 13(9Q21.12) MUTATED DEL PEAK 13(9Q21.12) WILD-TYPE
  FEMALE                            8                             80
  MALE                              6                             68
[1] 2 2
[1] FALSE
D19V5, binary
                                cls
clus                               0   1
  DEL PEAK 13(9Q21.12) MUTATED    12   2
  DEL PEAK 13(9Q21.12) WILD-TYPE 143   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(9Q21.12) MUTATED     12    2
  DEL PEAK 13(9Q21.12) WILD-TYPE  143    3
     clus
vv    DEL PEAK 13(9Q21.12) MUTATED DEL PEAK 13(9Q21.12) WILD-TYPE
  NO                            12                            143
  YES                            2                              3
[1] 2 2
[1] FALSE
D19V6, continuous
                                vv
clus                             PARAGANGLIOMA
  DEL PEAK 13(9Q21.12) MUTATED               2
  DEL PEAK 13(9Q21.12) WILD-TYPE            14
                                vv
clus                             PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK 13(9Q21.12) MUTATED                                               0
  DEL PEAK 13(9Q21.12) WILD-TYPE                                            11
                                vv
clus                             PHEOCHROMOCYTOMA
  DEL PEAK 13(9Q21.12) MUTATED                 12
  DEL PEAK 13(9Q21.12) WILD-TYPE              123
D19V7, multiclass
                                               clus
vv                                              DEL PEAK 13(9Q21.12) MUTATED
  PARAGANGLIOMA                                                            2
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                            0
  PHEOCHROMOCYTOMA                                                        12
                                               clus
vv                                              DEL PEAK 13(9Q21.12) WILD-TYPE
  PARAGANGLIOMA                                                             14
  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"
D19V8, continuous
[1] "Remove cluster labels:"       "DEL PEAK 13(9Q21.12) MUTATED"
clus
  DEL PEAK 13(9Q21.12) MUTATED DEL PEAK 13(9Q21.12) WILD-TYPE 
                             2                             16 
                    TCGA-QR-A70D                     TCGA-QR-A70P 
"DEL PEAK 13(9Q21.12) WILD-TYPE" "DEL PEAK 13(9Q21.12) WILD-TYPE" 
                    TCGA-WB-A814                     TCGA-WB-A820 
"DEL PEAK 13(9Q21.12) WILD-TYPE" "DEL PEAK 13(9Q21.12) WILD-TYPE" 
                    TCGA-XG-A823                     TCGA-PR-A5PG 
"DEL PEAK 13(9Q21.12) WILD-TYPE" "DEL PEAK 13(9Q21.12) WILD-TYPE" 
                    TCGA-PR-A5PH                     TCGA-QR-A702 
"DEL PEAK 13(9Q21.12) WILD-TYPE" "DEL PEAK 13(9Q21.12) WILD-TYPE" 
                    TCGA-QT-A69Q                     TCGA-RW-A680 
"DEL PEAK 13(9Q21.12) WILD-TYPE" "DEL PEAK 13(9Q21.12) WILD-TYPE" 
                    TCGA-RW-A686                     TCGA-RW-A8AZ 
"DEL PEAK 13(9Q21.12) WILD-TYPE" "DEL PEAK 13(9Q21.12) WILD-TYPE" 
                    TCGA-TT-A6YK                     TCGA-WB-A80Q 
"DEL PEAK 13(9Q21.12) WILD-TYPE" "DEL PEAK 13(9Q21.12) WILD-TYPE" 
                    TCGA-WB-A80Y                     TCGA-WB-A81W 
"DEL PEAK 13(9Q21.12) WILD-TYPE" "DEL PEAK 13(9Q21.12) WILD-TYPE" 
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(9Q21.12) MUTATED                                  0     0
  DEL PEAK 13(9Q21.12) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(9Q21.12) MUTATED                           2    12
  DEL PEAK 13(9Q21.12) WILD-TYPE                        17   122
D19V9, multiclass
                                  clus
vv                                 DEL PEAK 13(9Q21.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      12
                                  clus
vv                                 DEL PEAK 13(9Q21.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    17
  WHITE                                                       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(20) Variable = DEL PEAK 14(11P15.4) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 14(11P15.4) MUTATED   58  0
  DEL PEAK 14(11P15.4) WILD-TYPE 98  6
  DEL PEAK 14(11P15.4) MUTATED DEL PEAK 14(11P15.4) WILD-TYPE 
                            58                            104 
  DEL PEAK 14(11P15.4) MUTATED DEL PEAK 14(11P15.4) WILD-TYPE 
                             0                              6 
$`DEL PEAK 14(11P15.4) 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-SR-A6MV TCGA-WB-A814 TCGA-XG-A823 TCGA-P8-A6RX 
       30.51        18.94       121.05        74.04        20.19        17.75 
TCGA-P8-A6RY TCGA-QR-A6H2 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 
        5.88         9.93        31.53        15.58         1.28         4.11 
TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A7IN TCGA-QR-A7IP 
       13.12         9.01         1.41        14.20        12.39        17.95 
TCGA-QT-A5XL TCGA-QT-A5XN TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6YA 
        1.81        25.18        13.08        77.98         0.92        50.63 
TCGA-RW-A67X TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A68C TCGA-RW-A68D TCGA-S7-A7WP 
        2.93        37.51         1.05         6.28        72.79        31.04 
TCGA-S7-A7WT TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-SP-A6QD TCGA-SR-A6MT TCGA-SR-A6MU 
       42.77        23.21        17.95       109.25       106.75       110.53 
TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7UY 
       49.61        37.35        42.48        20.09        17.16        14.79 
TCGA-WB-A80M TCGA-WB-A816 TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81S 
        4.47        41.23        22.32        40.04        45.83        23.77 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       71.05        78.21        93.11       103.17 

$`DEL PEAK 14(11P15.4) 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-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q 
        3.12        19.86        17.69        43.07        48.53        24.82 
TCGA-WB-A820 TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-PR-A5PF TCGA-PR-A5PG 
       10.16        31.46        29.03         4.04        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-A6H3 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G 
        1.05         9.21        14.27       116.19         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70W TCGA-QR-A70X TCGA-QT-A5XJ TCGA-QT-A5XK 
       26.83        29.92        41.79         6.02        36.23         6.94 
TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-RT-A6Y9 TCGA-RT-A6YC 
        0.72         2.30         4.41         0.79       108.26         8.09 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A685 TCGA-RW-A686 
       86.89        19.86         7.10        47.64         0.85        19.30 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
        1.22        27.22        11.57         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WR TCGA-S7-A7WV TCGA-S7-A7WX 
       36.56        37.25        35.51        40.70        27.91        25.32 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
       24.20         9.73       114.77        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-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-TT-A6YO 
       81.93        24.66        26.20         4.34        19.92        13.32 
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-A815 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
       19.59        53.59        42.35        33.90        24.16        35.84 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81J TCGA-WB-A81N TCGA-WB-A81P 
       57.11        38.76        63.98        24.36        62.04        12.99 
TCGA-WB-A81R TCGA-WB-A81T 
        1.61        25.51 

  DEL PEAK 14(11P15.4) MUTATED DEL PEAK 14(11P15.4) WILD-TYPE 
                          0.92                           0.10 
  DEL PEAK 14(11P15.4) MUTATED DEL PEAK 14(11P15.4) WILD-TYPE 
                        121.05                         316.73 
  DEL PEAK 14(11P15.4) MUTATED DEL PEAK 14(11P15.4) WILD-TYPE 
                         24.41                          25.07 
[1] "0.9 - 121.0 (24.4)" "0.1 - 316.7 (25.1)"
[1] "hr="     "3.6e+08"
D20V2, continuous
D20V3, binary
                                cls
clus                              0  1
  DEL PEAK 14(11P15.4) MUTATED   45 13
  DEL PEAK 14(11P15.4) WILD-TYPE 89 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11P15.4) MUTATED     45   13
  DEL PEAK 14(11P15.4) WILD-TYPE   89   15
                    clus
vv                   DEL PEAK 14(11P15.4) MUTATED
  ADRENAL GLAND                                45
  EXTRA-ADRENAL SITE                           13
                    clus
vv                   DEL PEAK 14(11P15.4) WILD-TYPE
  ADRENAL GLAND                                  89
  EXTRA-ADRENAL SITE                             15
[1] 2 2
[1] FALSE
D20V4, binary
                                cls
clus                              0  1
  DEL PEAK 14(11P15.4) MUTATED   29 29
  DEL PEAK 14(11P15.4) WILD-TYPE 59 45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11P15.4) MUTATED     29   29
  DEL PEAK 14(11P15.4) WILD-TYPE   59   45
        clus
vv       DEL PEAK 14(11P15.4) MUTATED DEL PEAK 14(11P15.4) WILD-TYPE
  FEMALE                           29                             59
  MALE                             29                             45
[1] 2 2
[1] FALSE
D20V5, binary
                                cls
clus                              0  1
  DEL PEAK 14(11P15.4) MUTATED   56  2
  DEL PEAK 14(11P15.4) WILD-TYPE 99  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11P15.4) MUTATED     56    2
  DEL PEAK 14(11P15.4) WILD-TYPE   99    3
     clus
vv    DEL PEAK 14(11P15.4) MUTATED DEL PEAK 14(11P15.4) WILD-TYPE
  NO                            56                             99
  YES                            2                              3
[1] 2 2
[1] FALSE
D20V6, continuous
                                vv
clus                             PARAGANGLIOMA
  DEL PEAK 14(11P15.4) MUTATED               7
  DEL PEAK 14(11P15.4) WILD-TYPE             9
                                vv
clus                             PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK 14(11P15.4) MUTATED                                               6
  DEL PEAK 14(11P15.4) WILD-TYPE                                             5
                                vv
clus                             PHEOCHROMOCYTOMA
  DEL PEAK 14(11P15.4) MUTATED                 45
  DEL PEAK 14(11P15.4) WILD-TYPE               90
D20V7, multiclass
                                               clus
vv                                              DEL PEAK 14(11P15.4) MUTATED
  PARAGANGLIOMA                                                            7
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                            6
  PHEOCHROMOCYTOMA                                                        45
                                               clus
vv                                              DEL PEAK 14(11P15.4) WILD-TYPE
  PARAGANGLIOMA                                                              9
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                              5
  PHEOCHROMOCYTOMA                                                          90
[1] 3 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
  DEL PEAK 14(11P15.4) MUTATED                                  0     2
  DEL PEAK 14(11P15.4) WILD-TYPE                                1     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(11P15.4) MUTATED                           6    49
  DEL PEAK 14(11P15.4) WILD-TYPE                        13    85
D20V9, multiclass
                                  clus
vv                                 DEL PEAK 14(11P15.4) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      49
                                  clus
vv                                 DEL PEAK 14(11P15.4) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    13
  WHITE                                                        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(21) Variable = DEL PEAK 15(11Q22.1) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 15(11Q22.1) MUTATED    49   1
  DEL PEAK 15(11Q22.1) WILD-TYPE 107   5
  DEL PEAK 15(11Q22.1) MUTATED DEL PEAK 15(11Q22.1) WILD-TYPE 
                            50                            112 
  DEL PEAK 15(11Q22.1) MUTATED DEL PEAK 15(11Q22.1) WILD-TYPE 
                             1                              5 
$`DEL PEAK 15(11Q22.1) MUTATED`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A700 TCGA-RW-A68F TCGA-RW-A7CZ TCGA-S7-A7WQ 
       58.88        30.51        32.15        44.52        13.87        26.96 
TCGA-S7-A7WU TCGA-S7-A7X1 TCGA-WB-A814 TCGA-XG-A823 TCGA-P8-A6RX TCGA-P8-A6RY 
       30.51        18.94        74.04        20.19        17.75         5.88 
TCGA-PR-A5PF TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6H2 TCGA-QR-A6H5 TCGA-QR-A702 
       17.95        23.11         1.25         9.93        31.53         1.28 
TCGA-QR-A706 TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A7IN TCGA-QT-A5XL TCGA-QT-A5XO 
        4.11         1.41        14.20        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-A7WL TCGA-S7-A7WP TCGA-S7-A7WW 
       27.22         6.28         2.89        31.59        31.04        23.21 
TCGA-S7-A7X0 TCGA-SR-A6MT TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YO TCGA-TT-A6YP 
       17.95       106.75        49.61         4.34        13.32        42.48 
TCGA-W2-A7UY TCGA-WB-A815 TCGA-WB-A81D TCGA-WB-A81P TCGA-WB-A81S TCGA-WB-A81V 
       14.79        53.59        35.84        12.99        23.77        71.05 
TCGA-WB-A81W TCGA-WB-A821 
       78.21        93.11 

$`DEL PEAK 15(11Q22.1) WILD-TYPE`
TCGA-QR-A6H1 TCGA-QR-A70D TCGA-QR-A70P TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68G 
       14.17         0.23       117.14        25.05        23.90        41.88 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A817 TCGA-WB-A81E 
      121.05         3.12        19.86        17.69        43.07        48.53 
TCGA-WB-A81Q TCGA-WB-A820 TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-PR-A5PG 
       24.82        10.16        31.46        29.03         4.04        81.70 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 
       28.08        35.01       137.59        19.04         1.05         9.21 
TCGA-QR-A6H3 TCGA-QR-A6H6 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
       14.27        15.58       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-A7IP 
       29.92        13.12         9.01        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-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WR TCGA-S7-A7WT 
       20.09        36.56        37.25        35.51        40.70        42.77 
TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       27.91        25.32        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-TT-A6YK TCGA-TT-A6YN TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       26.20        37.35        19.92        20.09        17.16         1.18 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L 
       14.43        18.44        16.60        25.61        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-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81F 
       19.59        41.23        42.35        33.90        24.16        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-A81R TCGA-WB-A81T TCGA-WB-A822 
       62.04         1.61        25.51       103.17 

  DEL PEAK 15(11Q22.1) MUTATED DEL PEAK 15(11Q22.1) WILD-TYPE 
                          0.79                           0.10 
  DEL PEAK 15(11Q22.1) MUTATED DEL PEAK 15(11Q22.1) WILD-TYPE 
                        106.75                         316.73 
  DEL PEAK 15(11Q22.1) MUTATED DEL PEAK 15(11Q22.1) WILD-TYPE 
                        21.650                         25.415 
[1] "0.8 - 106.8 (21.6)" "0.1 - 316.7 (25.4)"
[1] "hr=" "1.6"
D21V2, continuous
D21V3, binary
                                cls
clus                              0  1
  DEL PEAK 15(11Q22.1) MUTATED   42  8
  DEL PEAK 15(11Q22.1) WILD-TYPE 92 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q22.1) MUTATED     42    8
  DEL PEAK 15(11Q22.1) WILD-TYPE   92   20
                    clus
vv                   DEL PEAK 15(11Q22.1) MUTATED
  ADRENAL GLAND                                42
  EXTRA-ADRENAL SITE                            8
                    clus
vv                   DEL PEAK 15(11Q22.1) WILD-TYPE
  ADRENAL GLAND                                  92
  EXTRA-ADRENAL SITE                             20
[1] 2 2
[1] FALSE
D21V4, binary
                                cls
clus                              0  1
  DEL PEAK 15(11Q22.1) MUTATED   28 22
  DEL PEAK 15(11Q22.1) WILD-TYPE 60 52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q22.1) MUTATED     28   22
  DEL PEAK 15(11Q22.1) WILD-TYPE   60   52
        clus
vv       DEL PEAK 15(11Q22.1) MUTATED DEL PEAK 15(11Q22.1) WILD-TYPE
  FEMALE                           28                             60
  MALE                             22                             52
[1] 2 2
[1] FALSE
D21V5, binary
                                cls
clus                               0   1
  DEL PEAK 15(11Q22.1) MUTATED    50   0
  DEL PEAK 15(11Q22.1) WILD-TYPE 105   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q22.1) MUTATED     50    0
  DEL PEAK 15(11Q22.1) WILD-TYPE  105    5
     clus
vv    DEL PEAK 15(11Q22.1) MUTATED DEL PEAK 15(11Q22.1) WILD-TYPE
  NO                            50                            105
  YES                            0                              5
[1] 2 2
[1] FALSE
D21V6, continuous
                                vv
clus                             PARAGANGLIOMA
  DEL PEAK 15(11Q22.1) MUTATED               4
  DEL PEAK 15(11Q22.1) WILD-TYPE            12
                                vv
clus                             PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK 15(11Q22.1) MUTATED                                               4
  DEL PEAK 15(11Q22.1) WILD-TYPE                                             7
                                vv
clus                             PHEOCHROMOCYTOMA
  DEL PEAK 15(11Q22.1) MUTATED                 42
  DEL PEAK 15(11Q22.1) WILD-TYPE               93
D21V7, multiclass
                                               clus
vv                                              DEL PEAK 15(11Q22.1) MUTATED
  PARAGANGLIOMA                                                            4
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                            4
  PHEOCHROMOCYTOMA                                                        42
                                               clus
vv                                              DEL PEAK 15(11Q22.1) WILD-TYPE
  PARAGANGLIOMA                                                             12
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                              7
  PHEOCHROMOCYTOMA                                                          93
[1] 3 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
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(11Q22.1) MUTATED                                  0     1
  DEL PEAK 15(11Q22.1) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(11Q22.1) MUTATED                           7    41
  DEL PEAK 15(11Q22.1) WILD-TYPE                        12    93
D21V9, multiclass
                                  clus
vv                                 DEL PEAK 15(11Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      41
                                  clus
vv                                 DEL PEAK 15(11Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                        93
[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 = DEL PEAK 16(12Q21.33) MUTATION ANALYSIS
D22V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 16(12Q21.33) MUTATED     8   0
  DEL PEAK 16(12Q21.33) WILD-TYPE 148   6
  DEL PEAK 16(12Q21.33) MUTATED DEL PEAK 16(12Q21.33) WILD-TYPE 
                              8                             154 
  DEL PEAK 16(12Q21.33) MUTATED DEL PEAK 16(12Q21.33) WILD-TYPE 
                              0                               6 
$`DEL PEAK 16(12Q21.33) MUTATED`
TCGA-QR-A700 TCGA-SR-A6MV TCGA-QR-A70R TCGA-QR-A70X TCGA-RT-A6YC TCGA-SP-A6QJ 
       32.15       121.05        14.20         6.02         8.09        15.52 
TCGA-TT-A6YJ TCGA-WB-A81S 
        4.34        23.77 

$`DEL PEAK 16(12Q21.33) 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-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-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-A70W TCGA-QR-A7IN TCGA-QR-A7IP 
       13.12         9.01         1.41        41.79        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-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 
       50.63        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-A6QK 
      114.77       109.25        82.62        79.46       110.04       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-A6YK TCGA-TT-A6YN 
      110.53        24.66        26.20        49.61        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-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-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 

  DEL PEAK 16(12Q21.33) MUTATED DEL PEAK 16(12Q21.33) WILD-TYPE 
                           4.34                            0.10 
  DEL PEAK 16(12Q21.33) MUTATED DEL PEAK 16(12Q21.33) WILD-TYPE 
                         121.05                          316.73 
  DEL PEAK 16(12Q21.33) MUTATED DEL PEAK 16(12Q21.33) WILD-TYPE 
                          14.86                           25.25 
[1] "4.3 - 121.0 (14.9)" "0.1 - 316.7 (25.2)"
[1] "hr="     "8.1e+07"
D22V2, continuous
D22V3, binary
                                 cls
clus                                0   1
  DEL PEAK 16(12Q21.33) MUTATED     7   1
  DEL PEAK 16(12Q21.33) WILD-TYPE 127  27
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(12Q21.33) MUTATED      7    1
  DEL PEAK 16(12Q21.33) WILD-TYPE  127   27
                    clus
vv                   DEL PEAK 16(12Q21.33) MUTATED
  ADRENAL GLAND                                  7
  EXTRA-ADRENAL SITE                             1
                    clus
vv                   DEL PEAK 16(12Q21.33) WILD-TYPE
  ADRENAL GLAND                                  127
  EXTRA-ADRENAL SITE                              27
[1] 2 2
[1] FALSE
D22V4, binary
                                 cls
clus                               0  1
  DEL PEAK 16(12Q21.33) MUTATED    5  3
  DEL PEAK 16(12Q21.33) WILD-TYPE 83 71
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(12Q21.33) MUTATED      5    3
  DEL PEAK 16(12Q21.33) WILD-TYPE   83   71
        clus
vv       DEL PEAK 16(12Q21.33) MUTATED DEL PEAK 16(12Q21.33) WILD-TYPE
  FEMALE                             5                              83
  MALE                               3                              71
[1] 2 2
[1] FALSE
D22V5, binary
                                 cls
clus                                0   1
  DEL PEAK 16(12Q21.33) MUTATED     7   1
  DEL PEAK 16(12Q21.33) WILD-TYPE 148   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(12Q21.33) MUTATED      7    1
  DEL PEAK 16(12Q21.33) WILD-TYPE  148    4
     clus
vv    DEL PEAK 16(12Q21.33) MUTATED DEL PEAK 16(12Q21.33) WILD-TYPE
  NO                              7                             148
  YES                             1                               4
[1] 2 2
[1] FALSE
D22V6, continuous
                                 vv
clus                              PARAGANGLIOMA
  DEL PEAK 16(12Q21.33) MUTATED               1
  DEL PEAK 16(12Q21.33) WILD-TYPE            15
                                 vv
clus                              PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK 16(12Q21.33) MUTATED                                               0
  DEL PEAK 16(12Q21.33) WILD-TYPE                                            11
                                 vv
clus                              PHEOCHROMOCYTOMA
  DEL PEAK 16(12Q21.33) MUTATED                  7
  DEL PEAK 16(12Q21.33) WILD-TYPE              128
D22V7, multiclass
                                               clus
vv                                              DEL PEAK 16(12Q21.33) MUTATED
  PARAGANGLIOMA                                                             1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                             0
  PHEOCHROMOCYTOMA                                                          7
                                               clus
vv                                              DEL PEAK 16(12Q21.33) WILD-TYPE
  PARAGANGLIOMA                                                              15
  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"
D22V8, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(12Q21.33) MUTATED                                  0     0
  DEL PEAK 16(12Q21.33) WILD-TYPE                                1     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(12Q21.33) MUTATED                           1     6
  DEL PEAK 16(12Q21.33) WILD-TYPE                        18   128
D22V9, multiclass
                                  clus
vv                                 DEL PEAK 16(12Q21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    1
  WHITE                                                        6
                                  clus
vv                                 DEL PEAK 16(12Q21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     18
  WHITE                                                        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(23) Variable = DEL PEAK 17(13Q22.3) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 17(13Q22.3) MUTATED     8   0
  DEL PEAK 17(13Q22.3) WILD-TYPE 148   6
  DEL PEAK 17(13Q22.3) MUTATED DEL PEAK 17(13Q22.3) WILD-TYPE 
                             8                            154 
  DEL PEAK 17(13Q22.3) MUTATED DEL PEAK 17(13Q22.3) WILD-TYPE 
                             0                              6 
$`DEL PEAK 17(13Q22.3) MUTATED`
TCGA-QR-A700 TCGA-RW-A68A TCGA-PR-A5PF TCGA-QR-A706 TCGA-QR-A70R TCGA-S7-A7WX 
       32.15        25.05        17.95         4.11        14.20        25.32 
TCGA-SP-A6QF TCGA-W2-A7H5 
       82.62        20.09 

$`DEL PEAK 17(13Q22.3) 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-A70C 
        9.93        14.27        31.53        15.58         1.28       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-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-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 

  DEL PEAK 17(13Q22.3) MUTATED DEL PEAK 17(13Q22.3) WILD-TYPE 
                          4.11                           0.10 
  DEL PEAK 17(13Q22.3) MUTATED DEL PEAK 17(13Q22.3) WILD-TYPE 
                         82.62                         316.73 
  DEL PEAK 17(13Q22.3) MUTATED DEL PEAK 17(13Q22.3) WILD-TYPE 
                         22.57                          25.00 
[1] "4.1 - 82.6 (22.6)"  "0.1 - 316.7 (25.0)"
[1] "hr="     "2.6e+07"
D23V2, continuous
D23V3, binary
                                cls
clus                               0   1
  DEL PEAK 17(13Q22.3) MUTATED     7   1
  DEL PEAK 17(13Q22.3) WILD-TYPE 127  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(13Q22.3) MUTATED      7    1
  DEL PEAK 17(13Q22.3) WILD-TYPE  127   27
                    clus
vv                   DEL PEAK 17(13Q22.3) MUTATED
  ADRENAL GLAND                                 7
  EXTRA-ADRENAL SITE                            1
                    clus
vv                   DEL PEAK 17(13Q22.3) WILD-TYPE
  ADRENAL GLAND                                 127
  EXTRA-ADRENAL SITE                             27
[1] 2 2
[1] FALSE
D23V4, binary
                                cls
clus                              0  1
  DEL PEAK 17(13Q22.3) MUTATED    4  4
  DEL PEAK 17(13Q22.3) WILD-TYPE 84 70
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(13Q22.3) MUTATED      4    4
  DEL PEAK 17(13Q22.3) WILD-TYPE   84   70
        clus
vv       DEL PEAK 17(13Q22.3) MUTATED DEL PEAK 17(13Q22.3) WILD-TYPE
  FEMALE                            4                             84
  MALE                              4                             70
[1] 2 2
[1] FALSE
D23V5, binary
                                cls
clus                               0   1
  DEL PEAK 17(13Q22.3) MUTATED     8   0
  DEL PEAK 17(13Q22.3) WILD-TYPE 147   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(13Q22.3) MUTATED      8    0
  DEL PEAK 17(13Q22.3) WILD-TYPE  147    5
     clus
vv    DEL PEAK 17(13Q22.3) MUTATED DEL PEAK 17(13Q22.3) WILD-TYPE
  NO                             8                            147
  YES                            0                              5
[1] 2 2
[1] FALSE
D23V6, continuous
                                vv
clus                             PARAGANGLIOMA
  DEL PEAK 17(13Q22.3) MUTATED               1
  DEL PEAK 17(13Q22.3) WILD-TYPE            15
                                vv
clus                             PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK 17(13Q22.3) MUTATED                                               0
  DEL PEAK 17(13Q22.3) WILD-TYPE                                            11
                                vv
clus                             PHEOCHROMOCYTOMA
  DEL PEAK 17(13Q22.3) MUTATED                  7
  DEL PEAK 17(13Q22.3) WILD-TYPE              128
D23V7, multiclass
                                               clus
vv                                              DEL PEAK 17(13Q22.3) MUTATED
  PARAGANGLIOMA                                                            1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                            0
  PHEOCHROMOCYTOMA                                                         7
                                               clus
vv                                              DEL PEAK 17(13Q22.3) WILD-TYPE
  PARAGANGLIOMA                                                             15
  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"
D23V8, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(13Q22.3) MUTATED                                  0     1
  DEL PEAK 17(13Q22.3) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(13Q22.3) MUTATED                           0     7
  DEL PEAK 17(13Q22.3) WILD-TYPE                        19   127
D23V9, multiclass
                                  clus
vv                                 DEL PEAK 17(13Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       7
                                  clus
vv                                 DEL PEAK 17(13Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    19
  WHITE                                                       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(24) Variable = DEL PEAK 18(16Q21) MUTATION ANALYSIS
D24V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 18(16Q21) MUTATED     5   0
  DEL PEAK 18(16Q21) WILD-TYPE 151   6
  DEL PEAK 18(16Q21) MUTATED DEL PEAK 18(16Q21) WILD-TYPE 
                           5                          157 
  DEL PEAK 18(16Q21) MUTATED DEL PEAK 18(16Q21) WILD-TYPE 
                           0                            6 
$`DEL PEAK 18(16Q21) MUTATED`
TCGA-QR-A700 TCGA-QT-A5XJ TCGA-QT-A69Q TCGA-SR-A6MT TCGA-WB-A81S 
       32.15        36.23         0.79       106.75        23.77 

$`DEL PEAK 18(16Q21) 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-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-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
        6.02        12.39        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-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 

  DEL PEAK 18(16Q21) MUTATED DEL PEAK 18(16Q21) WILD-TYPE 
                        0.79                         0.10 
  DEL PEAK 18(16Q21) MUTATED DEL PEAK 18(16Q21) WILD-TYPE 
                      106.75                       316.73 
  DEL PEAK 18(16Q21) MUTATED DEL PEAK 18(16Q21) WILD-TYPE 
                       32.15                        24.82 
[1] "0.8 - 106.8 (32.1)" "0.1 - 316.7 (24.8)"
[1] "hr="     "2.6e+07"
D24V2, continuous
D24V3, binary
                              cls
clus                             0   1
  DEL PEAK 18(16Q21) MUTATED     5   0
  DEL PEAK 18(16Q21) WILD-TYPE 129  28
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 18(16Q21) MUTATED      5    0
  DEL PEAK 18(16Q21) WILD-TYPE  129   28
                    clus
vv                   DEL PEAK 18(16Q21) MUTATED DEL PEAK 18(16Q21) WILD-TYPE
  ADRENAL GLAND                               5                          129
  EXTRA-ADRENAL SITE                          0                           28
[1] 2 2
[1] FALSE
D24V4, binary
                              cls
clus                            0  1
  DEL PEAK 18(16Q21) MUTATED    3  2
  DEL PEAK 18(16Q21) WILD-TYPE 85 72
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 18(16Q21) MUTATED      3    2
  DEL PEAK 18(16Q21) WILD-TYPE   85   72
        clus
vv       DEL PEAK 18(16Q21) MUTATED DEL PEAK 18(16Q21) WILD-TYPE
  FEMALE                          3                           85
  MALE                            2                           72
[1] 2 2
[1] FALSE
D24V5, binary
                              cls
clus                             0   1
  DEL PEAK 18(16Q21) MUTATED     5   0
  DEL PEAK 18(16Q21) WILD-TYPE 150   5
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 18(16Q21) MUTATED      5    0
  DEL PEAK 18(16Q21) WILD-TYPE  150    5
     clus
vv    DEL PEAK 18(16Q21) MUTATED DEL PEAK 18(16Q21) WILD-TYPE
  NO                           5                          150
  YES                          0                            5
[1] 2 2
[1] FALSE
D24V6, continuous
[1] "Remove cluster labels:"     "DEL PEAK 18(16Q21) MUTATED"
clus
  DEL PEAK 18(16Q21) MUTATED DEL PEAK 18(16Q21) WILD-TYPE 
                           1                           59 
                  TCGA-S7-A7WQ                   TCGA-S7-A7WU 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-S7-A7X1                   TCGA-SR-A6MV 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-WB-A817                   TCGA-WB-A81E 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-XG-A823                   TCGA-P7-A5NY 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-PR-A5PF                   TCGA-PR-A5PG 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-PR-A5PH                   TCGA-RT-A6YA 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-RT-A6YC                   TCGA-RX-A8JQ 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-S7-A7WL                   TCGA-S7-A7WM 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-S7-A7WN                   TCGA-S7-A7WO 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-S7-A7WP                   TCGA-S7-A7WR 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-S7-A7WT                   TCGA-S7-A7WV 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-S7-A7WW                   TCGA-S7-A7WX 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-S7-A7X0                   TCGA-S7-A7X2 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-SP-A6QC                   TCGA-SP-A6QD 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-SP-A6QF                   TCGA-SP-A6QG 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-SP-A6QI                   TCGA-SP-A6QJ 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-SP-A6QK                   TCGA-SR-A6MQ 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-SR-A6MS                   TCGA-SR-A6MY 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-SR-A6MZ                   TCGA-SR-A6N0 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-TT-A6YK                   TCGA-TT-A6YN 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-TT-A6YO                   TCGA-TT-A6YP 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-WB-A80K                   TCGA-WB-A80L 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-WB-A80Q                   TCGA-WB-A815 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-WB-A818                   TCGA-WB-A81D 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-WB-A81F                   TCGA-WB-A81G 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-WB-A81H                   TCGA-WB-A81I 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-WB-A81J                   TCGA-WB-A81K 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-WB-A81M                   TCGA-WB-A81N 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-WB-A81T                   TCGA-WB-A821 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-WB-A822 
"DEL PEAK 18(16Q21) WILD-TYPE" 
                              vv
clus                           PARAGANGLIOMA
  DEL PEAK 18(16Q21) MUTATED               0
  DEL PEAK 18(16Q21) WILD-TYPE            16
                              vv
clus                           PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK 18(16Q21) MUTATED                                               0
  DEL PEAK 18(16Q21) WILD-TYPE                                            11
                              vv
clus                           PHEOCHROMOCYTOMA
  DEL PEAK 18(16Q21) MUTATED                  5
  DEL PEAK 18(16Q21) WILD-TYPE              130
D24V7, multiclass
                                               clus
vv                                              DEL PEAK 18(16Q21) MUTATED
  PARAGANGLIOMA                                                          0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                          0
  PHEOCHROMOCYTOMA                                                       5
                                               clus
vv                                              DEL PEAK 18(16Q21) 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"
D24V8, continuous
[1] "Remove cluster labels:"     "DEL PEAK 18(16Q21) MUTATED"
clus
  DEL PEAK 18(16Q21) MUTATED DEL PEAK 18(16Q21) WILD-TYPE 
                           2                           16 
                  TCGA-QR-A70D                   TCGA-QR-A70P 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-WB-A814                   TCGA-WB-A820 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-XG-A823                   TCGA-PR-A5PG 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-PR-A5PH                   TCGA-QR-A702 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-QT-A5XP                   TCGA-RW-A680 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-RW-A686                   TCGA-RW-A8AZ 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-TT-A6YK                   TCGA-WB-A80Q 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                  TCGA-WB-A80Y                   TCGA-WB-A81W 
"DEL PEAK 18(16Q21) WILD-TYPE" "DEL PEAK 18(16Q21) WILD-TYPE" 
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(16Q21) MUTATED                                  0     0
  DEL PEAK 18(16Q21) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(16Q21) MUTATED                           1     4
  DEL PEAK 18(16Q21) WILD-TYPE                        18   130
D24V9, multiclass
                                  clus
vv                                 DEL PEAK 18(16Q21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 1
  WHITE                                                     4
                                  clus
vv                                 DEL PEAK 18(16Q21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     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(25) Variable = DEL PEAK 19(17P13.2) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(17P13.2) MUTATED   62  2
  DEL PEAK 19(17P13.2) WILD-TYPE 94  4
  DEL PEAK 19(17P13.2) MUTATED DEL PEAK 19(17P13.2) WILD-TYPE 
                            64                             98 
  DEL PEAK 19(17P13.2) MUTATED DEL PEAK 19(17P13.2) WILD-TYPE 
                             2                              4 
$`DEL PEAK 19(17P13.2) 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-A7WR TCGA-S7-A7WT TCGA-S7-A7WW TCGA-S7-A7WX 
       31.59        36.56        40.70        42.77        23.21        25.32 
TCGA-S7-A7X2 TCGA-SP-A6QD TCGA-SP-A6QJ TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       24.20       109.25        15.52         0.10        51.22        68.61 
TCGA-SR-A6MT TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-W2-A7HA TCGA-W2-A7HC 
      106.75         4.34        37.35        19.92         1.18        14.43 
TCGA-W2-A7UY TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A80Y 
       14.79         4.73        25.51       316.73        29.16        19.59 
TCGA-WB-A815 TCGA-WB-A818 TCGA-WB-A81J TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       53.59        42.35        24.36        45.83        62.04        12.99 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81W TCGA-WB-A822 
       23.77        25.51        78.21       103.17 

$`DEL PEAK 19(17P13.2) 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-A7WV TCGA-S7-A7X0 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QF 
       31.04        27.91        17.95         9.73       114.77        82.62 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MS TCGA-SR-A6MU 
       79.46       110.04       111.25         1.41        81.93       110.53 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
       24.66        26.20        49.61        13.32        42.48        20.09 
TCGA-W2-A7H7 TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L 
       17.16        18.44        16.60        25.61        41.26        34.26 
TCGA-WB-A80M TCGA-WB-A80Q TCGA-WB-A816 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
        4.47       127.56        41.23        33.90        24.16        35.84 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81R 
       57.11        38.76        63.98        22.32        40.04         1.61 
TCGA-WB-A81V TCGA-WB-A821 
       71.05        93.11 

  DEL PEAK 19(17P13.2) MUTATED DEL PEAK 19(17P13.2) WILD-TYPE 
                          0.10                           0.23 
  DEL PEAK 19(17P13.2) MUTATED DEL PEAK 19(17P13.2) WILD-TYPE 
                        316.73                         137.59 
  DEL PEAK 19(17P13.2) MUTATED DEL PEAK 19(17P13.2) WILD-TYPE 
                        24.590                         25.905 
[1] "0.1 - 316.7 (24.6)" "0.2 - 137.6 (25.9)"
[1] "hr=" "1.1"
D25V2, continuous
D25V3, binary
                                cls
clus                              0  1
  DEL PEAK 19(17P13.2) MUTATED   59  5
  DEL PEAK 19(17P13.2) WILD-TYPE 75 23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(17P13.2) MUTATED     59    5
  DEL PEAK 19(17P13.2) WILD-TYPE   75   23
                    clus
vv                   DEL PEAK 19(17P13.2) MUTATED
  ADRENAL GLAND                                59
  EXTRA-ADRENAL SITE                            5
                    clus
vv                   DEL PEAK 19(17P13.2) WILD-TYPE
  ADRENAL GLAND                                  75
  EXTRA-ADRENAL SITE                             23
[1] 2 2
[1] FALSE
D25V4, binary
                                cls
clus                              0  1
  DEL PEAK 19(17P13.2) MUTATED   33 31
  DEL PEAK 19(17P13.2) WILD-TYPE 55 43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(17P13.2) MUTATED     33   31
  DEL PEAK 19(17P13.2) WILD-TYPE   55   43
        clus
vv       DEL PEAK 19(17P13.2) MUTATED DEL PEAK 19(17P13.2) WILD-TYPE
  FEMALE                           33                             55
  MALE                             31                             43
[1] 2 2
[1] FALSE
D25V5, binary
                                cls
clus                              0  1
  DEL PEAK 19(17P13.2) MUTATED   60  3
  DEL PEAK 19(17P13.2) WILD-TYPE 95  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(17P13.2) MUTATED     60    3
  DEL PEAK 19(17P13.2) WILD-TYPE   95    2
     clus
vv    DEL PEAK 19(17P13.2) MUTATED DEL PEAK 19(17P13.2) WILD-TYPE
  NO                            60                             95
  YES                            3                              2
[1] 2 2
[1] FALSE
D25V6, continuous
                                vv
clus                             PARAGANGLIOMA
  DEL PEAK 19(17P13.2) MUTATED               3
  DEL PEAK 19(17P13.2) WILD-TYPE            13
                                vv
clus                             PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK 19(17P13.2) MUTATED                                               2
  DEL PEAK 19(17P13.2) WILD-TYPE                                             9
                                vv
clus                             PHEOCHROMOCYTOMA
  DEL PEAK 19(17P13.2) MUTATED                 59
  DEL PEAK 19(17P13.2) WILD-TYPE               76
D25V7, multiclass
                                               clus
vv                                              DEL PEAK 19(17P13.2) MUTATED
  PARAGANGLIOMA                                                            3
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                            2
  PHEOCHROMOCYTOMA                                                        59
                                               clus
vv                                              DEL PEAK 19(17P13.2) WILD-TYPE
  PARAGANGLIOMA                                                             13
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                              9
  PHEOCHROMOCYTOMA                                                          76
[1] 3 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
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(17P13.2) MUTATED                                  1     2
  DEL PEAK 19(17P13.2) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(17P13.2) MUTATED                           4    55
  DEL PEAK 19(17P13.2) WILD-TYPE                        15    79
D25V9, multiclass
                                  clus
vv                                 DEL PEAK 19(17P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      55
                                  clus
vv                                 DEL PEAK 19(17P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                        79
[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 = DEL PEAK 20(17Q11.2) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(17Q11.2) MUTATED    39   3
  DEL PEAK 20(17Q11.2) WILD-TYPE 117   3
  DEL PEAK 20(17Q11.2) MUTATED DEL PEAK 20(17Q11.2) WILD-TYPE 
                            42                            120 
  DEL PEAK 20(17Q11.2) MUTATED DEL PEAK 20(17Q11.2) WILD-TYPE 
                             3                              3 
$`DEL PEAK 20(17Q11.2) MUTATED`
TCGA-QR-A700 TCGA-S7-A7WQ TCGA-S7-A7X1 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 
       32.15        26.96        18.94        48.53        24.82        10.16 
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A702 TCGA-QR-A70H TCGA-QR-A70J TCGA-QT-A5XN 
       23.11         1.25         1.28        26.83        13.12        25.18 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-RT-A6YA TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
        4.41         0.79        50.63        19.86         2.93         7.10 
TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A7D0 TCGA-S7-A7WL 
        0.85         1.22        27.22         6.28        11.57        31.59 
TCGA-S7-A7WM TCGA-S7-A7WR TCGA-S7-A7WX TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MT 
       36.56        40.70        25.32         0.10        51.22       106.75 
TCGA-TT-A6YJ TCGA-W2-A7UY TCGA-WB-A80N TCGA-WB-A80Y TCGA-WB-A818 TCGA-WB-A81D 
        4.34        14.79         4.73        19.59        42.35        35.84 
TCGA-WB-A81F TCGA-WB-A81H TCGA-WB-A81J TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81S 
       57.11        63.98        24.36        62.04        12.99        23.77 

$`DEL PEAK 20(17Q11.2) 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-XG-A823 
        3.12        19.86        17.69        74.04        43.07        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-A6GT TCGA-QR-A6GX TCGA-QR-A6GY 
       81.70        28.08        35.01       137.59        19.04         1.05 
TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A706 
        9.21         9.93        14.27        31.53        15.58         4.11 
TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70I TCGA-QR-A70K TCGA-QR-A70N 
      116.19         6.31         2.33        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-A5XO TCGA-QT-A7U0 TCGA-RM-A68T 
        6.94         1.81         0.72         2.30        13.08        77.98 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A680 TCGA-RW-A681 
        0.92       108.26         8.09        86.89        47.64        37.51 
TCGA-RW-A684 TCGA-RW-A686 TCGA-RW-A68D TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WN 
        1.05        19.30        72.79         2.89        20.09        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 
       35.51        31.04        42.77        27.91        23.21        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-A6MQ TCGA-SR-A6MS 
      110.04        15.52       111.25         1.41        68.61        81.93 
TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YN 
      110.53        24.66        26.20        49.61        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-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       18.44        16.60        25.61        41.26        34.26         4.47 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A815 TCGA-WB-A816 
       25.51       316.73       127.56        29.16        53.59        41.23 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81G TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M 
       33.90        24.16        38.76        22.32        40.04        45.83 
TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
        1.61        25.51        71.05        78.21        93.11       103.17 

  DEL PEAK 20(17Q11.2) MUTATED DEL PEAK 20(17Q11.2) WILD-TYPE 
                          0.10                           0.23 
  DEL PEAK 20(17Q11.2) MUTATED DEL PEAK 20(17Q11.2) WILD-TYPE 
                        106.75                         316.73 
  DEL PEAK 20(17Q11.2) MUTATED DEL PEAK 20(17Q11.2) WILD-TYPE 
                         23.44                          25.56 
[1] "0.1 - 106.8 (23.4)" "0.2 - 316.7 (25.6)"
[1] "hr=" "4.7"
D26V2, continuous
D26V3, binary
                                cls
clus                              0  1
  DEL PEAK 20(17Q11.2) MUTATED   40  2
  DEL PEAK 20(17Q11.2) WILD-TYPE 94 26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(17Q11.2) MUTATED     40    2
  DEL PEAK 20(17Q11.2) WILD-TYPE   94   26
                    clus
vv                   DEL PEAK 20(17Q11.2) MUTATED
  ADRENAL GLAND                                40
  EXTRA-ADRENAL SITE                            2
                    clus
vv                   DEL PEAK 20(17Q11.2) WILD-TYPE
  ADRENAL GLAND                                  94
  EXTRA-ADRENAL SITE                             26
[1] 2 2
[1] FALSE
D26V4, binary
                                cls
clus                              0  1
  DEL PEAK 20(17Q11.2) MUTATED   24 18
  DEL PEAK 20(17Q11.2) WILD-TYPE 64 56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(17Q11.2) MUTATED     24   18
  DEL PEAK 20(17Q11.2) WILD-TYPE   64   56
        clus
vv       DEL PEAK 20(17Q11.2) MUTATED DEL PEAK 20(17Q11.2) WILD-TYPE
  FEMALE                           24                             64
  MALE                             18                             56
[1] 2 2
[1] FALSE
D26V5, binary
                                cls
clus                               0   1
  DEL PEAK 20(17Q11.2) MUTATED    40   1
  DEL PEAK 20(17Q11.2) WILD-TYPE 115   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(17Q11.2) MUTATED     40    1
  DEL PEAK 20(17Q11.2) WILD-TYPE  115    4
     clus
vv    DEL PEAK 20(17Q11.2) MUTATED DEL PEAK 20(17Q11.2) WILD-TYPE
  NO                            40                            115
  YES                            1                              4
[1] 2 2
[1] FALSE
D26V6, continuous
                                vv
clus                             PARAGANGLIOMA
  DEL PEAK 20(17Q11.2) MUTATED               1
  DEL PEAK 20(17Q11.2) WILD-TYPE            15
                                vv
clus                             PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK 20(17Q11.2) MUTATED                                               1
  DEL PEAK 20(17Q11.2) WILD-TYPE                                            10
                                vv
clus                             PHEOCHROMOCYTOMA
  DEL PEAK 20(17Q11.2) MUTATED                 40
  DEL PEAK 20(17Q11.2) WILD-TYPE               95
D26V7, multiclass
                                               clus
vv                                              DEL PEAK 20(17Q11.2) MUTATED
  PARAGANGLIOMA                                                            1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                            1
  PHEOCHROMOCYTOMA                                                        40
                                               clus
vv                                              DEL PEAK 20(17Q11.2) WILD-TYPE
  PARAGANGLIOMA                                                             15
  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"
D26V8, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(17Q11.2) MUTATED                                  0     0
  DEL PEAK 20(17Q11.2) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(17Q11.2) MUTATED                           2    39
  DEL PEAK 20(17Q11.2) WILD-TYPE                        17    95
D26V9, multiclass
                                  clus
vv                                 DEL PEAK 20(17Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      39
                                  clus
vv                                 DEL PEAK 20(17Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    17
  WHITE                                                        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(27) Variable = DEL PEAK 21(22Q13.31) MUTATION ANALYSIS
D27V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 21(22Q13.31) MUTATED   60  5
  DEL PEAK 21(22Q13.31) WILD-TYPE 96  1
  DEL PEAK 21(22Q13.31) MUTATED DEL PEAK 21(22Q13.31) WILD-TYPE 
                             65                              97 
  DEL PEAK 21(22Q13.31) MUTATED DEL PEAK 21(22Q13.31) WILD-TYPE 
                              5                               1 
$`DEL PEAK 21(22Q13.31) 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-PR-A5PH 
       10.16        20.19         4.04         5.88        17.95        28.08 
TCGA-QR-A6GR TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G 
       23.11        15.58         1.28       116.19         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70K TCGA-QR-A70W TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XO 
       26.83         9.01        41.79         6.94         1.81         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-RT-A6Y9 TCGA-RW-A67Y TCGA-RW-A681 TCGA-RW-A686 
        4.41         0.79       108.26         7.10        37.51        19.30 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WR TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SP-A6QF 
       31.59        36.56        40.70        25.32        24.20        82.62 
TCGA-SP-A6QG TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       79.46        15.52       111.25         0.10        51.22        68.61 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YK TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HC 
       24.66        26.20        37.35        20.09         1.18        14.43 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7UY TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80V 
       18.44        16.60        14.79         4.73        25.51        29.16 
TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
       19.59        53.59        42.35        33.90        24.16        35.84 
TCGA-WB-A81H TCGA-WB-A81N TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81W 
       63.98        62.04         1.61        25.51        78.21 

$`DEL PEAK 21(22Q13.31) 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-QR-A6GO TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX 
       17.75        81.70        35.01         1.25       137.59        19.04 
TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A706 
        1.05         9.21         9.93        14.27        31.53         4.11 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70X TCGA-QR-A7IN 
       29.92        13.12         1.41        14.20         6.02        12.39 
TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A7U0 TCGA-RM-A68T 
       17.95        36.23         0.72        25.18        13.08        77.98 
TCGA-RM-A68W TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
        0.92        50.63         8.09        86.89        19.86         2.93 
TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C 
       47.64         1.05         0.85         1.22        27.22         6.28 
TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WO 
       72.79        11.57         2.89        20.09        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-SA-A6C2 
       31.04        42.77        27.91        23.21        17.95         9.73 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QI TCGA-SQ-A6I4 TCGA-SR-A6MS TCGA-SR-A6MT 
      114.77       109.25       110.04         1.41        81.93       106.75 
TCGA-SR-A6MU TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
      110.53        49.61         4.34        19.92        13.32        42.48 
TCGA-W2-A7H7 TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80P 
       17.16        25.61        41.26        34.26         4.47       316.73 
TCGA-WB-A80Q TCGA-WB-A816 TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81I TCGA-WB-A81J 
      127.56        41.23        57.11        38.76        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81P TCGA-WB-A81S TCGA-WB-A81V TCGA-WB-A821 
       40.04        45.83        12.99        23.77        71.05        93.11 
TCGA-WB-A822 
      103.17 

  DEL PEAK 21(22Q13.31) MUTATED DEL PEAK 21(22Q13.31) WILD-TYPE 
                           0.10                            0.23 
  DEL PEAK 21(22Q13.31) MUTATED DEL PEAK 21(22Q13.31) WILD-TYPE 
                         117.14                          316.73 
  DEL PEAK 21(22Q13.31) MUTATED DEL PEAK 21(22Q13.31) WILD-TYPE 
                          24.16                           27.22 
[1] "0.1 - 117.1 (24.2)" "0.2 - 316.7 (27.2)"
[1] "hr=" "9.6"
D27V2, continuous
D27V3, binary
                                 cls
clus                               0  1
  DEL PEAK 21(22Q13.31) MUTATED   58  7
  DEL PEAK 21(22Q13.31) WILD-TYPE 76 21
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(22Q13.31) MUTATED     58    7
  DEL PEAK 21(22Q13.31) WILD-TYPE   76   21
                    clus
vv                   DEL PEAK 21(22Q13.31) MUTATED
  ADRENAL GLAND                                 58
  EXTRA-ADRENAL SITE                             7
                    clus
vv                   DEL PEAK 21(22Q13.31) WILD-TYPE
  ADRENAL GLAND                                   76
  EXTRA-ADRENAL SITE                              21
[1] 2 2
[1] FALSE
D27V4, binary
                                 cls
clus                               0  1
  DEL PEAK 21(22Q13.31) MUTATED   36 29
  DEL PEAK 21(22Q13.31) WILD-TYPE 52 45
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(22Q13.31) MUTATED     36   29
  DEL PEAK 21(22Q13.31) WILD-TYPE   52   45
        clus
vv       DEL PEAK 21(22Q13.31) MUTATED DEL PEAK 21(22Q13.31) WILD-TYPE
  FEMALE                            36                              52
  MALE                              29                              45
[1] 2 2
[1] FALSE
D27V5, binary
                                 cls
clus                               0  1
  DEL PEAK 21(22Q13.31) MUTATED   62  2
  DEL PEAK 21(22Q13.31) WILD-TYPE 93  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(22Q13.31) MUTATED     62    2
  DEL PEAK 21(22Q13.31) WILD-TYPE   93    3
     clus
vv    DEL PEAK 21(22Q13.31) MUTATED DEL PEAK 21(22Q13.31) WILD-TYPE
  NO                             62                              93
  YES                             2                               3
[1] 2 2
[1] FALSE
D27V6, continuous
                                 vv
clus                              PARAGANGLIOMA
  DEL PEAK 21(22Q13.31) MUTATED               6
  DEL PEAK 21(22Q13.31) WILD-TYPE            10
                                 vv
clus                              PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK 21(22Q13.31) MUTATED                                               1
  DEL PEAK 21(22Q13.31) WILD-TYPE                                            10
                                 vv
clus                              PHEOCHROMOCYTOMA
  DEL PEAK 21(22Q13.31) MUTATED                 58
  DEL PEAK 21(22Q13.31) WILD-TYPE               77
D27V7, multiclass
                                               clus
vv                                              DEL PEAK 21(22Q13.31) MUTATED
  PARAGANGLIOMA                                                             6
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                             1
  PHEOCHROMOCYTOMA                                                         58
                                               clus
vv                                              DEL PEAK 21(22Q13.31) WILD-TYPE
  PARAGANGLIOMA                                                              10
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                              10
  PHEOCHROMOCYTOMA                                                           77
[1] 3 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
  DEL PEAK 21(22Q13.31) MUTATED                                  1     3
  DEL PEAK 21(22Q13.31) WILD-TYPE                                0     2
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(22Q13.31) MUTATED                           6    55
  DEL PEAK 21(22Q13.31) WILD-TYPE                        13    79
D27V9, multiclass
                                  clus
vv                                 DEL PEAK 21(22Q13.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                    6
  WHITE                                                       55
                                  clus
vv                                 DEL PEAK 21(22Q13.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          2
  BLACK OR AFRICAN AMERICAN                                     13
  WHITE                                                         79
[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 = DEL PEAK 22(XP21.1) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(XP21.1) MUTATED    45   1
  DEL PEAK 22(XP21.1) WILD-TYPE 111   5
  DEL PEAK 22(XP21.1) MUTATED DEL PEAK 22(XP21.1) WILD-TYPE 
                           46                           116 
  DEL PEAK 22(XP21.1) MUTATED DEL PEAK 22(XP21.1) WILD-TYPE 
                            1                             5 
$`DEL PEAK 22(XP21.1) MUTATED`
TCGA-RW-A68A TCGA-S7-A7WQ TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF TCGA-WB-A81E 
       25.05        26.96         3.12        19.86        17.69        48.53 
TCGA-QR-A6GO TCGA-QR-A6GT TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A70H TCGA-QR-A70K 
       35.01       137.59        15.58         1.28        26.83         9.01 
TCGA-QR-A70R TCGA-QR-A70W TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK 
       14.20        41.79        12.39        17.95        36.23         6.94 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RT-A6YA TCGA-RW-A67Y TCGA-RW-A689 
       25.18         2.30         0.79        50.63         7.10        27.22 
TCGA-RW-A68C TCGA-S7-A7WR TCGA-SP-A6QG TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MY 
        6.28        40.70        79.46         0.10        68.61        24.66 
TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC 
        4.34        19.92        42.48        17.16         1.18        14.43 
TCGA-W2-A7HD TCGA-W2-A7UY TCGA-WB-A80M TCGA-WB-A80V TCGA-WB-A815 TCGA-WB-A819 
       18.44        14.79         4.47        29.16        53.59        33.90 
TCGA-WB-A81F TCGA-WB-A81K TCGA-WB-A81R TCGA-WB-A81W 
       57.11        40.04         1.61        78.21 

$`DEL PEAK 22(XP21.1) 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-SR-A6MV TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 
      121.05        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-A6GR TCGA-QR-A6GS TCGA-QR-A6GX TCGA-QR-A6GY 
       81.70        28.08        23.11         1.25        19.04         1.05 
TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A706 TCGA-QR-A70C 
        9.21         9.93        14.27        31.53         4.11       116.19 
TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70X 
        6.31         2.33        29.92        13.12         1.41         6.02 
TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        1.81         0.72         4.41        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A680 
      108.26         8.09        86.89        19.86         2.93        47.64 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68D 
       37.51         1.05         0.85        19.30         1.22        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-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       35.51        31.04        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-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MS 
      110.04        15.52       111.25         1.41        51.22        81.93 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YO 
      106.75       110.53        26.20        49.61        37.35        13.32 
TCGA-W2-A7H5 TCGA-W2-A7HE TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80N 
       20.09        16.60        25.61        41.26        34.26         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A816 TCGA-WB-A818 
       25.51       316.73       127.56        19.59        41.23        42.35 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       24.16        35.84        38.76        63.98        22.32        24.36 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       45.83        62.04        12.99        23.77        25.51        71.05 
TCGA-WB-A821 TCGA-WB-A822 
       93.11       103.17 

  DEL PEAK 22(XP21.1) MUTATED DEL PEAK 22(XP21.1) WILD-TYPE 
                         0.10                          0.23 
  DEL PEAK 22(XP21.1) MUTATED DEL PEAK 22(XP21.1) WILD-TYPE 
                       137.59                        316.73 
  DEL PEAK 22(XP21.1) MUTATED DEL PEAK 22(XP21.1) WILD-TYPE 
                        19.89                         25.51 
[1] "0.1 - 137.6 (19.9)" "0.2 - 316.7 (25.5)"
[1] "hr=" "1.7"
D28V2, continuous
D28V3, binary
                               cls
clus                             0  1
  DEL PEAK 22(XP21.1) MUTATED   38  8
  DEL PEAK 22(XP21.1) WILD-TYPE 96 20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(XP21.1) MUTATED     38    8
  DEL PEAK 22(XP21.1) WILD-TYPE   96   20
                    clus
vv                   DEL PEAK 22(XP21.1) MUTATED DEL PEAK 22(XP21.1) WILD-TYPE
  ADRENAL GLAND                               38                            96
  EXTRA-ADRENAL SITE                           8                            20
[1] 2 2
[1] FALSE
D28V4, binary
                               cls
clus                             0  1
  DEL PEAK 22(XP21.1) MUTATED   25 21
  DEL PEAK 22(XP21.1) WILD-TYPE 63 53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(XP21.1) MUTATED     25   21
  DEL PEAK 22(XP21.1) WILD-TYPE   63   53
        clus
vv       DEL PEAK 22(XP21.1) MUTATED DEL PEAK 22(XP21.1) WILD-TYPE
  FEMALE                          25                            63
  MALE                            21                            53
[1] 2 2
[1] FALSE
D28V5, binary
                               cls
clus                              0   1
  DEL PEAK 22(XP21.1) MUTATED    45   0
  DEL PEAK 22(XP21.1) WILD-TYPE 110   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(XP21.1) MUTATED     45    0
  DEL PEAK 22(XP21.1) WILD-TYPE  110    5
     clus
vv    DEL PEAK 22(XP21.1) MUTATED DEL PEAK 22(XP21.1) WILD-TYPE
  NO                           45                           110
  YES                           0                             5
[1] 2 2
[1] FALSE
D28V6, continuous
                               vv
clus                            PARAGANGLIOMA
  DEL PEAK 22(XP21.1) MUTATED               6
  DEL PEAK 22(XP21.1) WILD-TYPE            10
                               vv
clus                            PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  DEL PEAK 22(XP21.1) MUTATED                                               1
  DEL PEAK 22(XP21.1) WILD-TYPE                                            10
                               vv
clus                            PHEOCHROMOCYTOMA
  DEL PEAK 22(XP21.1) MUTATED                 39
  DEL PEAK 22(XP21.1) WILD-TYPE               96
D28V7, multiclass
                                               clus
vv                                              DEL PEAK 22(XP21.1) MUTATED
  PARAGANGLIOMA                                                           6
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                           1
  PHEOCHROMOCYTOMA                                                       39
                                               clus
vv                                              DEL PEAK 22(XP21.1) WILD-TYPE
  PARAGANGLIOMA                                                            10
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                            10
  PHEOCHROMOCYTOMA                                                         96
[1] 3 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
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(XP21.1) MUTATED                                  1     1
  DEL PEAK 22(XP21.1) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(XP21.1) MUTATED                           6    37
  DEL PEAK 22(XP21.1) WILD-TYPE                        13    97
D28V9, multiclass
                                  clus
vv                                 DEL PEAK 22(XP21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     37
                                  clus
vv                                 DEL PEAK 22(XP21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                       97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
