[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/22569699/transformed.cor.cli.txt"

nPatients in clinical file=179, in cluster file=179, common to both=179
[1] "Reduce the number of clustering variables from 10 to 8."
[1]   8 179
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            18            161 
  HRAS MUTATED HRAS WILD-TYPE 
            18            161 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           15           164 
  NF1 MUTATED NF1 WILD-TYPE 
           15           164 
[1] "EPAS1 MUTATION ANALYSIS"
[1] 3
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              8             171 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              8             171 
[1] "NUDT11 MUTATION ANALYSIS"
[1] 3
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               5              174 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               5              174 
[1] "RET MUTATION ANALYSIS"
[1] 3
  RET MUTATED RET WILD-TYPE 
            6           173 
  RET MUTATED RET WILD-TYPE 
            6           173 
[1] "SHROOM4 MUTATION ANALYSIS"
[1] 3
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                3               176 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                3               176 
[1] "AMMECR1 MUTATION ANALYSIS"
[1] 3
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                3               176 
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                3               176 
[1] "GPR128 MUTATION ANALYSIS"
[1] 3
  GPR128 MUTATED GPR128 WILD-TYPE 
               4              175 
  GPR128 MUTATED GPR128 WILD-TYPE 
               4              175 
[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 179 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=59,	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=164,	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=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 179 columns, 1 survival variables, and 9 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"                       
[9] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=59, 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
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = HRAS MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  HRAS MUTATED    18   0
  HRAS WILD-TYPE 155   6
  HRAS MUTATED HRAS WILD-TYPE 
            18            161 
  HRAS MUTATED HRAS WILD-TYPE 
             0              6 
$`HRAS MUTATED`
TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A6GW TCGA-QR-A6H4 TCGA-QR-A70M TCGA-QR-A70W 
        4.04        81.70        16.14        87.48        33.99        41.79 
TCGA-S7-A7WN TCGA-S7-A7WR TCGA-SP-A6QF TCGA-SP-A6QJ TCGA-SR-A6MQ TCGA-SR-A6MY 
       37.25        40.70        82.62        15.52        68.61        24.66 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A81R TCGA-WB-A81T 
       14.43        18.44         4.73        25.51         1.61        25.51 

$`HRAS WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A6ZZ TCGA-QR-A700 TCGA-QR-A703 
       58.88        30.51        14.17         1.58        32.15        38.37 
TCGA-QR-A705 TCGA-QR-A70D TCGA-QR-A70O TCGA-QR-A70P TCGA-QR-A70T TCGA-RW-A68A 
       10.42         0.23         3.65       117.14         8.78        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-SP-A6QH TCGA-SR-A6MR TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB 
       18.94        72.43        79.20       121.05         3.12        19.86 
TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 
       17.69        74.04        43.07        48.53        24.82        10.16 
TCGA-XG-A823 TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY 
       20.19        26.89        31.46        29.03        17.75         5.88 
TCGA-PR-A5PF TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       17.95        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
       19.04         1.05         9.21         9.93        14.27        31.53 
TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A707 TCGA-QR-A708 TCGA-QR-A70A 
       15.58         1.28         4.11        13.08         1.15        69.67 
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-A70Q TCGA-QR-A70R TCGA-QR-A70U TCGA-QR-A70V 
        9.01         1.41         4.60        14.20        48.43         0.07 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
        6.02        12.39        17.95        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       77.98         0.92       108.26        50.63         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       19.86         2.93         7.10        47.64        37.51         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D 
        0.85        19.30         1.22        27.22         6.28        72.79 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WO 
       11.57         2.89        20.09        31.59        36.56        35.51 
TCGA-S7-A7WP TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       31.04        42.77        27.91        23.21        25.32        17.95 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI 
       24.20         9.73       114.77       109.25        79.46       110.04 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MS TCGA-SR-A6MT 
      111.25         1.41         0.10        51.22        81.93       106.75 
TCGA-SR-A6MU TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
      110.53        26.20        49.61         4.34        37.35        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HE 
       13.32        42.48        20.09        17.16         1.18        16.60 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80P 
       25.61        14.79        41.26        34.26         4.47       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-A81S TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       23.77        71.05        78.21        93.11       103.17 

  HRAS MUTATED HRAS WILD-TYPE 
          1.61           0.07 
  HRAS MUTATED HRAS WILD-TYPE 
         87.48         316.73 
  HRAS MUTATED HRAS WILD-TYPE 
         25.51          24.36 
[1] "1.6 - 87.5 (25.5)"  "0.1 - 316.7 (24.4)"
[1] "hr="     "7.9e+07"
D1V2, continuous
D1V3, binary
                cls
clus               0   1
  HRAS MUTATED    17   1
  HRAS WILD-TYPE 130  31
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED     17    1
  HRAS WILD-TYPE  130   31
                    clus
vv                   HRAS MUTATED HRAS WILD-TYPE
  ADRENAL GLAND                17            130
  EXTRA-ADRENAL SITE            1             31
[1] 2 2
[1] FALSE
D1V4, binary
                cls
clus              0  1
  HRAS MUTATED   11  7
  HRAS WILD-TYPE 90 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED     11    7
  HRAS WILD-TYPE   90   71
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  FEMALE           11             90
  MALE              7             71
[1] 2 2
[1] FALSE
D1V5, binary
                cls
clus               0   1
  HRAS MUTATED    18   0
  HRAS WILD-TYPE 154   5
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED     18    0
  HRAS WILD-TYPE  154    5
     clus
vv    HRAS MUTATED HRAS WILD-TYPE
  NO            18            154
  YES            0              5
[1] 2 2
[1] FALSE
D1V6, continuous
                vv
clus             PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  HRAS MUTATED               1                                             0
  HRAS WILD-TYPE            17                                            13
                vv
clus             PHEOCHROMOCYTOMA
  HRAS MUTATED                 17
  HRAS WILD-TYPE              131
D1V7, multiclass
                                               clus
vv                                              HRAS MUTATED HRAS WILD-TYPE
  PARAGANGLIOMA                                            1             17
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA            0             13
  PHEOCHROMOCYTOMA                                        17            131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, continuous
[1] "Remove cluster labels:" "HRAS MUTATED"          
clus
  HRAS MUTATED HRAS WILD-TYPE 
             1             20 
    TCGA-QR-A705     TCGA-QR-A70D     TCGA-QR-A70P     TCGA-QR-A70T 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-SR-A6MR     TCGA-WB-A814     TCGA-WB-A820     TCGA-XG-A823 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-PR-A5PH     TCGA-QR-A702     TCGA-QT-A5XJ     TCGA-QT-A5XP 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-QT-A69Q     TCGA-RW-A680     TCGA-RW-A686     TCGA-RW-A8AZ 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-TT-A6YK     TCGA-WB-A80Q     TCGA-WB-A80Y     TCGA-WB-A81W 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HRAS MUTATED                                  0     2
  HRAS WILD-TYPE                                1     4
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HRAS MUTATED                           0    16
  HRAS WILD-TYPE                        20   132
D1V9, multiclass
                                  clus
vv                                 HRAS MUTATED HRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              4
  BLACK OR AFRICAN AMERICAN                   0             20
  WHITE                                      16            132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
                cls
clus               0   1
  HRAS MUTATED     0  17
  HRAS WILD-TYPE   5 121
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0   17
  HRAS WILD-TYPE    5  121
                        clus
vv                       HRAS MUTATED HRAS WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO           17            121
[1] 2 2
[1] FALSE

Clustering(2) Variable = NF1 MUTATION ANALYSIS
D2V1, survival
               sevent
clus2             0   1
  NF1 MUTATED    15   0
  NF1 WILD-TYPE 158   6
  NF1 MUTATED NF1 WILD-TYPE 
           15           164 
  NF1 MUTATED NF1 WILD-TYPE 
            0             6 
$`NF1 MUTATED`
TCGA-QR-A6GS TCGA-QR-A702 TCGA-QR-A70V TCGA-RT-A6YA TCGA-RW-A67Y TCGA-RW-A685 
        1.25         1.28         0.07        50.63         7.10         0.85 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A7D0 TCGA-S7-A7WL TCGA-S7-A7WM TCGA-SQ-A6I6 
        1.22        27.22        11.57        31.59        36.56         0.10 
TCGA-WB-A818 TCGA-WB-A81P TCGA-WB-A81V 
       42.35        12.99        71.05 

$`NF1 WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A6ZZ TCGA-QR-A700 TCGA-QR-A703 
       58.88        30.51        14.17         1.58        32.15        38.37 
TCGA-QR-A705 TCGA-QR-A70D TCGA-QR-A70O TCGA-QR-A70P TCGA-QR-A70T TCGA-RW-A68A 
       10.42         0.23         3.65       117.14         8.78        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-SP-A6QH TCGA-SR-A6MR TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB 
       18.94        72.43        79.20       121.05         3.12        19.86 
TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 
       17.69        74.04        43.07        48.53        24.82        10.16 
TCGA-XG-A823 TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX 
       20.19        26.89        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-A6GT TCGA-QR-A6GW TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 
      137.59        16.14        19.04         1.05         9.21         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H4 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A706 TCGA-QR-A707 
       14.27        87.48        31.53        15.58         4.11        13.08 
TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.15        69.67       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70M TCGA-QR-A70N TCGA-QR-A70Q 
       29.92        13.12         9.01        33.99         1.41         4.60 
TCGA-QR-A70R TCGA-QR-A70U TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
       14.20        48.43        41.79         6.02        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       36.23         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        4.41         0.79        13.08        77.98         0.92       108.26 
TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A680 TCGA-RW-A681 
        8.09        86.89        19.86         2.93        47.64        37.51 
TCGA-RW-A684 TCGA-RW-A686 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A8AZ TCGA-RX-A8JQ 
        1.05        19.30         6.28        72.79         2.89        20.09 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV 
       37.25        35.51        31.04        40.70        42.77        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC 
       23.21        25.32        17.95        24.20         9.73       114.77 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      109.25        82.62        79.46       110.04        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
        1.41        51.22        68.61        81.93       106.75       110.53 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        26.20        49.61         4.34        37.35        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-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-A819 TCGA-WB-A81A TCGA-WB-A81D 
       19.59        53.59        41.23        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-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81W 
       45.83        62.04         1.61        23.77        25.51        78.21 
TCGA-WB-A821 TCGA-WB-A822 
       93.11       103.17 

  NF1 MUTATED NF1 WILD-TYPE 
         0.07          0.23 
  NF1 MUTATED NF1 WILD-TYPE 
        71.05        316.73 
  NF1 MUTATED NF1 WILD-TYPE 
       11.570        25.115 
[1] "0.1 - 71.0 (11.6)"  "0.2 - 316.7 (25.1)"
[1] "hr="     "2.7e+07"
D2V2, continuous
D2V3, binary
               cls
clus              0   1
  NF1 MUTATED    14   1
  NF1 WILD-TYPE 133  31
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     14    1
  NF1 WILD-TYPE  133   31
                    clus
vv                   NF1 MUTATED NF1 WILD-TYPE
  ADRENAL GLAND               14           133
  EXTRA-ADRENAL SITE           1            31
[1] 2 2
[1] FALSE
D2V4, binary
               cls
clus             0  1
  NF1 MUTATED    9  6
  NF1 WILD-TYPE 92 72
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      9    6
  NF1 WILD-TYPE   92   72
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE           9            92
  MALE             6            72
[1] 2 2
[1] FALSE
D2V5, binary
               cls
clus              0   1
  NF1 MUTATED    14   0
  NF1 WILD-TYPE 158   5
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     14    0
  NF1 WILD-TYPE  158    5
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO           14           158
  YES           0             5
[1] 2 2
[1] FALSE
D2V6, continuous
               vv
clus            PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  NF1 MUTATED               1                                             0
  NF1 WILD-TYPE            17                                            13
               vv
clus            PHEOCHROMOCYTOMA
  NF1 MUTATED                 14
  NF1 WILD-TYPE              134
D2V7, multiclass
                                               clus
vv                                              NF1 MUTATED NF1 WILD-TYPE
  PARAGANGLIOMA                                           1            17
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA           0            13
  PHEOCHROMOCYTOMA                                       14           134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, continuous
[1] "Remove cluster labels:" "NF1 MUTATED"           
clus
  NF1 MUTATED NF1 WILD-TYPE 
            1            20 
   TCGA-QR-A705    TCGA-QR-A70D    TCGA-QR-A70P    TCGA-QR-A70T    TCGA-SR-A6MR 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-WB-A814    TCGA-WB-A820    TCGA-XG-A823    TCGA-PR-A5PG    TCGA-PR-A5PH 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-QT-A5XJ    TCGA-QT-A5XP    TCGA-QT-A69Q    TCGA-RW-A680    TCGA-RW-A686 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-RW-A8AZ    TCGA-TT-A6YK    TCGA-WB-A80Q    TCGA-WB-A80Y    TCGA-WB-A81W 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF1 MUTATED                                  0     0
  NF1 WILD-TYPE                                1     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED                           0    14
  NF1 WILD-TYPE                        20   134
D2V9, multiclass
                                  clus
vv                                 NF1 MUTATED NF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             6
  BLACK OR AFRICAN AMERICAN                  0            20
  WHITE                                     14           134
[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"
D2V10, binary
               cls
clus              0   1
  NF1 MUTATED     1   8
  NF1 WILD-TYPE   4 130
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      1    8
  NF1 WILD-TYPE    4  130
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               1             4
  NOT HISPANIC OR LATINO           8           130
[1] 2 2
[1] FALSE

Clustering(3) Variable = EPAS1 MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2               0   1
  EPAS1 MUTATED     8   0
  EPAS1 WILD-TYPE 165   6
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              8             171 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              0               6 
$`EPAS1 MUTATED`
TCGA-SR-A6MV TCGA-WB-A814 TCGA-QR-A7IN TCGA-QT-A5XL TCGA-QT-A7U0 TCGA-RW-A68D 
      121.05        74.04        12.39         1.81        13.08        72.79 
TCGA-S7-A7X0 TCGA-WB-A821 
       17.95        93.11 

$`EPAS1 WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A6ZZ TCGA-QR-A700 TCGA-QR-A703 
       58.88        30.51        14.17         1.58        32.15        38.37 
TCGA-QR-A705 TCGA-QR-A70D TCGA-QR-A70O TCGA-QR-A70P TCGA-QR-A70T TCGA-RW-A68A 
       10.42         0.23         3.65       117.14         8.78        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-SP-A6QH TCGA-SR-A6MR TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       18.94        72.43        79.20         3.12        19.86        17.69 
TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 TCGA-P7-A5NX 
       43.07        48.53        24.82        10.16        20.19        26.89 
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-A6GW TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 
       16.14        19.04         1.05         9.21         9.93        14.27 
TCGA-QR-A6H4 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A707 
       87.48        31.53        15.58         1.28         4.11        13.08 
TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.15        69.67       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70M TCGA-QR-A70N TCGA-QR-A70Q 
       29.92        13.12         9.01        33.99         1.41         4.60 
TCGA-QR-A70R TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IP 
       14.20        48.43         0.07        41.79         6.02        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP 
       36.23         6.94         0.72        25.18         2.30         4.41 
TCGA-QT-A69Q TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC 
        0.79        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-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
       11.57         2.89        20.09        31.59        36.56        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW 
       35.51        31.04        40.70        42.77        27.91        23.21 
TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
       25.32        24.20         9.73       114.77       109.25        82.62 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       79.46       110.04        15.52       111.25         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MY 
       51.22        68.61        81.93       106.75       110.53        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       26.20        49.61         4.34        37.35        19.92        13.32 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD 
       42.48        20.09        17.16         1.18        14.43        18.44 
TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       16.60        25.61        14.79        41.26        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73        25.51       316.73       127.56        29.16        19.59 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
       53.59        41.23        42.35        33.90        24.16        35.84 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       57.11        38.76        63.98        22.32        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       45.83        62.04        12.99         1.61        23.77        25.51 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 
       71.05        78.21       103.17 

  EPAS1 MUTATED EPAS1 WILD-TYPE 
           1.81            0.07 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
         121.05          316.73 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
          45.37           24.82 
[1] "1.8 - 121.0 (45.4)" "0.1 - 316.7 (24.8)"
[1] "hr="     "8.1e+07"
D3V2, continuous
D3V3, binary
                 cls
clus                0   1
  EPAS1 MUTATED     4   4
  EPAS1 WILD-TYPE 143  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPAS1 MUTATED      4    4
  EPAS1 WILD-TYPE  143   28
                    clus
vv                   EPAS1 MUTATED EPAS1 WILD-TYPE
  ADRENAL GLAND                  4             143
  EXTRA-ADRENAL SITE             4              28
[1] 2 2
[1] FALSE
D3V4, binary
                 cls
clus               0  1
  EPAS1 MUTATED    6  2
  EPAS1 WILD-TYPE 95 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPAS1 MUTATED      6    2
  EPAS1 WILD-TYPE   95   76
        clus
vv       EPAS1 MUTATED EPAS1 WILD-TYPE
  FEMALE             6              95
  MALE               2              76
[1] 2 2
[1] FALSE
D3V5, binary
                 cls
clus                0   1
  EPAS1 MUTATED     7   1
  EPAS1 WILD-TYPE 165   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPAS1 MUTATED      7    1
  EPAS1 WILD-TYPE  165    4
     clus
vv    EPAS1 MUTATED EPAS1 WILD-TYPE
  NO              7             165
  YES             1               4
[1] 2 2
[1] FALSE
D3V6, continuous
                 vv
clus              PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  EPAS1 MUTATED               1                                             3
  EPAS1 WILD-TYPE            17                                            10
                 vv
clus              PHEOCHROMOCYTOMA
  EPAS1 MUTATED                  4
  EPAS1 WILD-TYPE              144
D3V7, multiclass
                                               clus
vv                                              EPAS1 MUTATED EPAS1 WILD-TYPE
  PARAGANGLIOMA                                             1              17
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA             3              10
  PHEOCHROMOCYTOMA                                          4             144
[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:" "EPAS1 MUTATED"         
clus
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              1              20 
     TCGA-QR-A705      TCGA-QR-A70D      TCGA-QR-A70P      TCGA-QR-A70T 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-SR-A6MR      TCGA-WB-A820      TCGA-XG-A823      TCGA-PR-A5PG 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-PR-A5PH      TCGA-QR-A702      TCGA-QT-A5XJ      TCGA-QT-A5XP 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-QT-A69Q      TCGA-RW-A680      TCGA-RW-A686      TCGA-RW-A8AZ 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-TT-A6YK      TCGA-WB-A80Q      TCGA-WB-A80Y      TCGA-WB-A81W 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPAS1 MUTATED                                  0     1
  EPAS1 WILD-TYPE                                1     5
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EPAS1 MUTATED                           2     5
  EPAS1 WILD-TYPE                        18   143
D3V9, multiclass
                                  clus
vv                                 EPAS1 MUTATED EPAS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               5
  BLACK OR AFRICAN AMERICAN                    2              18
  WHITE                                        5             143
[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"
D3V10, binary
                 cls
clus                0   1
  EPAS1 MUTATED     0   6
  EPAS1 WILD-TYPE   5 132
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPAS1 MUTATED      0    6
  EPAS1 WILD-TYPE    5  132
                        clus
vv                       EPAS1 MUTATED EPAS1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6             132
[1] 2 2
[1] FALSE

Clustering(4) Variable = NUDT11 MUTATION ANALYSIS
D4V1, survival
                  sevent
clus2                0   1
  NUDT11 MUTATED     5   0
  NUDT11 WILD-TYPE 168   6
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               5              174 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               0                6 
$`NUDT11 MUTATED`
TCGA-RW-A68F TCGA-QR-A70I TCGA-QT-A5XN TCGA-WB-A818 TCGA-WB-A81N 
       44.52        29.92        25.18        42.35        62.04 

$`NUDT11 WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A6ZZ TCGA-QR-A700 TCGA-QR-A703 
       58.88        30.51        14.17         1.58        32.15        38.37 
TCGA-QR-A705 TCGA-QR-A70D TCGA-QR-A70O TCGA-QR-A70P TCGA-QR-A70T TCGA-RW-A68A 
       10.42         0.23         3.65       117.14         8.78        25.05 
TCGA-RW-A68B TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7X1 
       23.90        41.88        13.87        26.96        30.51        18.94 
TCGA-SP-A6QH TCGA-SR-A6MR TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB TCGA-W2-A7HF 
       72.43        79.20       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-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY 
       26.89        31.46        29.03         4.04        17.75         5.88 
TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS 
       17.95        81.70        28.08        35.01        23.11         1.25 
TCGA-QR-A6GT TCGA-QR-A6GW TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 
      137.59        16.14        19.04         1.05         9.21         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H4 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 
       14.27        87.48        31.53        15.58         1.28         4.11 
TCGA-QR-A707 TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G 
       13.08         1.15        69.67       116.19         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70M TCGA-QR-A70N TCGA-QR-A70Q 
       26.83        13.12         9.01        33.99         1.41         4.60 
TCGA-QR-A70R TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
       14.20        48.43         0.07        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-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       50.63         8.09        86.89        19.86         2.93         7.10 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
       47.64        37.51         1.05         0.85        19.30         1.22 
TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       27.22         6.28        72.79        11.57         2.89        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR 
       31.59        36.56        37.25        35.51        31.04        40.70 
TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 
       42.77        27.91        23.21        25.32        17.95        24.20 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
        9.73       114.77       109.25        82.62        79.46       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       15.52       111.25         1.41         0.10        51.22        68.61 
TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
       81.93       106.75       110.53        24.66        26.20        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        37.35        19.92        13.32        42.48        20.09 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       17.16         1.18        14.43        18.44        16.60        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       14.79        41.26        34.26         4.47         4.73        25.51 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 
      316.73       127.56        29.16        19.59        53.59        41.23 
TCGA-WB-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-A81P TCGA-WB-A81R 
       22.32        24.36        40.04        45.83        12.99         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       23.77        25.51        71.05        78.21        93.11       103.17 

  NUDT11 MUTATED NUDT11 WILD-TYPE 
           25.18             0.07 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           62.04           316.73 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           42.35            24.28 
[1] "25.2 - 62.0 (42.4)" "0.1 - 316.7 (24.3)"
[1] "hr="     "2.6e+07"
D4V2, continuous
D4V3, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     4   1
  NUDT11 WILD-TYPE 143  31
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      4    1
  NUDT11 WILD-TYPE  143   31
                    clus
vv                   NUDT11 MUTATED NUDT11 WILD-TYPE
  ADRENAL GLAND                   4              143
  EXTRA-ADRENAL SITE              1               31
[1] 2 2
[1] FALSE
D4V4, binary
                  cls
clus                0  1
  NUDT11 MUTATED    3  2
  NUDT11 WILD-TYPE 98 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      3    2
  NUDT11 WILD-TYPE   98   76
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  FEMALE              3               98
  MALE                2               76
[1] 2 2
[1] FALSE
D4V5, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     5   0
  NUDT11 WILD-TYPE 167   5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      5    0
  NUDT11 WILD-TYPE  167    5
     clus
vv    NUDT11 MUTATED NUDT11 WILD-TYPE
  NO               5              167
  YES              0                5
[1] 2 2
[1] FALSE
D4V6, continuous
[1] "Remove cluster labels:" "NUDT11 MUTATED"        
clus
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               2               60 
      TCGA-S7-A7WQ       TCGA-S7-A7WU       TCGA-S7-A7X1       TCGA-SR-A6MR 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-SR-A6MV       TCGA-WB-A817       TCGA-WB-A81E       TCGA-XG-A823 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-P7-A5NX       TCGA-P7-A5NY       TCGA-PR-A5PF       TCGA-PR-A5PG 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-PR-A5PH       TCGA-RT-A6YA       TCGA-RT-A6YC       TCGA-RX-A8JQ 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-S7-A7WL       TCGA-S7-A7WM       TCGA-S7-A7WN       TCGA-S7-A7WO 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-S7-A7WP       TCGA-S7-A7WR       TCGA-S7-A7WT       TCGA-S7-A7WV 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-S7-A7WW       TCGA-S7-A7WX       TCGA-S7-A7X0       TCGA-S7-A7X2 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-SP-A6QC       TCGA-SP-A6QD       TCGA-SP-A6QF       TCGA-SP-A6QG 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-SP-A6QI       TCGA-SP-A6QJ       TCGA-SP-A6QK       TCGA-SR-A6MQ 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-SR-A6MS       TCGA-SR-A6MY       TCGA-SR-A6MZ       TCGA-SR-A6N0 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-TT-A6YK       TCGA-TT-A6YN       TCGA-TT-A6YO       TCGA-TT-A6YP 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-WB-A80K       TCGA-WB-A80L       TCGA-WB-A80Q       TCGA-WB-A815 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-WB-A81D       TCGA-WB-A81F       TCGA-WB-A81G       TCGA-WB-A81H 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-WB-A81I       TCGA-WB-A81J       TCGA-WB-A81K       TCGA-WB-A81M 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-WB-A81S       TCGA-WB-A81T       TCGA-WB-A821       TCGA-WB-A822 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
                  vv
clus               PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  NUDT11 MUTATED               1                                             0
  NUDT11 WILD-TYPE            17                                            13
                  vv
clus               PHEOCHROMOCYTOMA
  NUDT11 MUTATED                  4
  NUDT11 WILD-TYPE              144
D4V7, multiclass
                                               clus
vv                                              NUDT11 MUTATED NUDT11 WILD-TYPE
  PARAGANGLIOMA                                              1               17
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA              0               13
  PHEOCHROMOCYTOMA                                           4              144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUDT11 MUTATED                                  0     0
  NUDT11 WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUDT11 MUTATED                           2     3
  NUDT11 WILD-TYPE                        18   145
D4V9, multiclass
                                  clus
vv                                 NUDT11 MUTATED NUDT11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                6
  BLACK OR AFRICAN AMERICAN                     2               18
  WHITE                                         3              145
[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"
D4V10, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     0   4
  NUDT11 WILD-TYPE   5 134
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      0    4
  NUDT11 WILD-TYPE    5  134
                        clus
vv                       NUDT11 MUTATED NUDT11 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4              134
[1] 2 2
[1] FALSE

Clustering(5) Variable = RET MUTATION ANALYSIS
D5V1, survival
               sevent
clus2             0   1
  RET MUTATED     6   0
  RET WILD-TYPE 167   6
  RET MUTATED RET WILD-TYPE 
            6           173 
  RET MUTATED RET WILD-TYPE 
            0             6 
$`RET MUTATED`
TCGA-QT-A5XK TCGA-QT-A5XM TCGA-SP-A6QK TCGA-W2-A7HA TCGA-WB-A80V TCGA-WB-A819 
        6.94         0.72       111.25         1.18        29.16        33.90 

$`RET WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A6ZZ TCGA-QR-A700 TCGA-QR-A703 
       58.88        30.51        14.17         1.58        32.15        38.37 
TCGA-QR-A705 TCGA-QR-A70D TCGA-QR-A70O TCGA-QR-A70P TCGA-QR-A70T TCGA-RW-A68A 
       10.42         0.23         3.65       117.14         8.78        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-SP-A6QH TCGA-SR-A6MR TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB 
       18.94        72.43        79.20       121.05         3.12        19.86 
TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 
       17.69        74.04        43.07        48.53        24.82        10.16 
TCGA-XG-A823 TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX 
       20.19        26.89        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-A6GW TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 
        1.25       137.59        16.14        19.04         1.05         9.21 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H4 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 
        9.93        14.27        87.48        31.53        15.58         1.28 
TCGA-QR-A706 TCGA-QR-A707 TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C TCGA-QR-A70E 
        4.11        13.08         1.15        69.67       116.19         6.31 
TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70M 
        2.33        26.83        29.92        13.12         9.01        33.99 
TCGA-QR-A70N TCGA-QR-A70Q TCGA-QR-A70R TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70W 
        1.41         4.60        14.20        48.43         0.07        41.79 
TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A5XN 
        6.02        12.39        17.95        36.23         1.81        25.18 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        2.30         4.41         0.79        13.08        77.98         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
      108.26        50.63         8.09        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 
        7.10        47.64        37.51         1.05         0.85        19.30 
TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ 
        1.22        27.22         6.28        72.79        11.57         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        36.56        37.25        35.51        31.04 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       40.70        42.77        27.91        23.21        25.32        17.95 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       24.20         9.73       114.77       109.25        82.62        79.46 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
      110.04        15.52         1.41         0.10        51.22        68.61 
TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
       81.93       106.75       110.53        24.66        26.20        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        37.35        19.92        13.32        42.48        20.09 
TCGA-W2-A7H7 TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY 
       17.16        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-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A81A 
      127.56        19.59        53.59        41.23        42.35        24.16 
TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       35.84        57.11        38.76        63.98        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S 
       40.04        45.83        62.04        12.99         1.61        23.77 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       25.51        71.05        78.21        93.11       103.17 

  RET MUTATED RET WILD-TYPE 
         0.72          0.07 
  RET MUTATED RET WILD-TYPE 
       111.25        316.73 
  RET MUTATED RET WILD-TYPE 
        18.05         24.82 
[1] "0.7 - 111.2 (18.1)" "0.1 - 316.7 (24.8)"
[1] "hr="     "9300000"
D5V2, continuous
D5V3, binary
               cls
clus              0   1
  RET MUTATED     6   0
  RET WILD-TYPE 141  32
[1] "tbl2"
               cls
clus            [,1] [,2]
  RET MUTATED      6    0
  RET WILD-TYPE  141   32
                    clus
vv                   RET MUTATED RET WILD-TYPE
  ADRENAL GLAND                6           141
  EXTRA-ADRENAL SITE           0            32
[1] 2 2
[1] FALSE
D5V4, binary
               cls
clus             0  1
  RET MUTATED    4  2
  RET WILD-TYPE 97 76
[1] "tbl2"
               cls
clus            [,1] [,2]
  RET MUTATED      4    2
  RET WILD-TYPE   97   76
        clus
vv       RET MUTATED RET WILD-TYPE
  FEMALE           4            97
  MALE             2            76
[1] 2 2
[1] FALSE
D5V5, binary
               cls
clus              0   1
  RET MUTATED     6   0
  RET WILD-TYPE 166   5
[1] "tbl2"
               cls
clus            [,1] [,2]
  RET MUTATED      6    0
  RET WILD-TYPE  166    5
     clus
vv    RET MUTATED RET WILD-TYPE
  NO            6           166
  YES           0             5
[1] 2 2
[1] FALSE
D5V6, continuous
[1] "Remove cluster labels:" "RET MUTATED"           
clus
  RET MUTATED RET WILD-TYPE 
            1            61 
   TCGA-S7-A7WQ    TCGA-S7-A7WU    TCGA-S7-A7X1    TCGA-SR-A6MR    TCGA-SR-A6MV 
"RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" 
   TCGA-WB-A817    TCGA-WB-A81E    TCGA-XG-A823    TCGA-P7-A5NX    TCGA-P7-A5NY 
"RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" 
   TCGA-PR-A5PF    TCGA-PR-A5PG    TCGA-PR-A5PH    TCGA-RT-A6YA    TCGA-RT-A6YC 
"RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" 
   TCGA-RX-A8JQ    TCGA-S7-A7WL    TCGA-S7-A7WM    TCGA-S7-A7WN    TCGA-S7-A7WO 
"RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" 
   TCGA-S7-A7WP    TCGA-S7-A7WR    TCGA-S7-A7WT    TCGA-S7-A7WV    TCGA-S7-A7WW 
"RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" 
   TCGA-S7-A7WX    TCGA-S7-A7X0    TCGA-S7-A7X2    TCGA-SP-A6QC    TCGA-SP-A6QD 
"RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" 
   TCGA-SP-A6QF    TCGA-SP-A6QG    TCGA-SP-A6QI    TCGA-SP-A6QJ    TCGA-SR-A6MQ 
"RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" 
   TCGA-SR-A6MS    TCGA-SR-A6MY    TCGA-SR-A6MZ    TCGA-SR-A6N0    TCGA-TT-A6YK 
"RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" 
   TCGA-TT-A6YN    TCGA-TT-A6YO    TCGA-TT-A6YP    TCGA-WB-A80K    TCGA-WB-A80L 
"RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" 
   TCGA-WB-A80Q    TCGA-WB-A815    TCGA-WB-A818    TCGA-WB-A81D    TCGA-WB-A81F 
"RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" 
   TCGA-WB-A81G    TCGA-WB-A81H    TCGA-WB-A81I    TCGA-WB-A81J    TCGA-WB-A81K 
"RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" 
   TCGA-WB-A81M    TCGA-WB-A81N    TCGA-WB-A81S    TCGA-WB-A81T    TCGA-WB-A821 
"RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" "RET WILD-TYPE" 
   TCGA-WB-A822 
"RET WILD-TYPE" 
               vv
clus            PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  RET MUTATED               0                                             0
  RET WILD-TYPE            18                                            13
               vv
clus            PHEOCHROMOCYTOMA
  RET MUTATED                  6
  RET WILD-TYPE              142
D5V7, multiclass
                                               clus
vv                                              RET MUTATED RET WILD-TYPE
  PARAGANGLIOMA                                           0            18
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA           0            13
  PHEOCHROMOCYTOMA                                        6           142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RET MUTATED                                  1     1
  RET WILD-TYPE                                0     5
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  RET MUTATED                           1     3
  RET WILD-TYPE                        19   145
D5V9, multiclass
                                  clus
vv                                 RET MUTATED RET WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           1             0
  ASIAN                                      1             5
  BLACK OR AFRICAN AMERICAN                  1            19
  WHITE                                      3           145
[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"
D5V10, binary
               cls
clus              0   1
  RET MUTATED     0   4
  RET WILD-TYPE   5 134
[1] "tbl2"
               cls
clus            [,1] [,2]
  RET MUTATED      0    4
  RET WILD-TYPE    5  134
                        clus
vv                       RET MUTATED RET WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           4           134
[1] 2 2
[1] FALSE

Clustering(6) Variable = SHROOM4 MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  SHROOM4 MUTATED     3   0
  SHROOM4 WILD-TYPE 170   6
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                3               176 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                0                 6 
$`SHROOM4 MUTATED`
TCGA-QR-A70Q TCGA-S7-A7WN TCGA-WB-A816 
        4.60        37.25        41.23 

$`SHROOM4 WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A6ZZ TCGA-QR-A700 TCGA-QR-A703 
       58.88        30.51        14.17         1.58        32.15        38.37 
TCGA-QR-A705 TCGA-QR-A70D TCGA-QR-A70O TCGA-QR-A70P TCGA-QR-A70T TCGA-RW-A68A 
       10.42         0.23         3.65       117.14         8.78        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-SP-A6QH TCGA-SR-A6MR TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB 
       18.94        72.43        79.20       121.05         3.12        19.86 
TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 
       17.69        74.04        43.07        48.53        24.82        10.16 
TCGA-XG-A823 TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX 
       20.19        26.89        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-A6GW TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 
        1.25       137.59        16.14        19.04         1.05         9.21 
TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H4 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 
        9.93        14.27        87.48        31.53        15.58         1.28 
TCGA-QR-A706 TCGA-QR-A707 TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C TCGA-QR-A70E 
        4.11        13.08         1.15        69.67       116.19         6.31 
TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70M 
        2.33        26.83        29.92        13.12         9.01        33.99 
TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70W TCGA-QR-A70X 
        1.41        14.20        48.43         0.07        41.79         6.02 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       12.39        17.95        36.23         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
       25.18         2.30         4.41         0.79        13.08        77.98 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92       108.26        50.63         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 
        2.93         7.10        47.64        37.51         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 
       19.30         1.22        27.22         6.28        72.79        11.57 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WO TCGA-S7-A7WP 
        2.89        20.09        31.59        36.56        35.51        31.04 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       40.70        42.77        27.91        23.21        25.32        17.95 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
       24.20         9.73       114.77       109.25        82.62        79.46 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
      110.04        15.52       111.25         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ 
       68.61        81.93       106.75       110.53        24.66        26.20 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        37.35        19.92        13.32        42.48 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       20.09        17.16         1.18        14.43        18.44        16.60 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        14.79        41.26        34.26         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 
       25.51       316.73       127.56        29.16        19.59        53.59 
TCGA-WB-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 

  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
             4.60              0.07 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
            41.23            316.73 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
            37.25             24.74 
[1] "4.6 - 41.2 (37.2)"  "0.1 - 316.7 (24.7)"
[1] "hr="     "9200000"
D6V2, continuous
D6V3, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED     2   1
  SHROOM4 WILD-TYPE 145  31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      2    1
  SHROOM4 WILD-TYPE  145   31
                    clus
vv                   SHROOM4 MUTATED SHROOM4 WILD-TYPE
  ADRENAL GLAND                    2               145
  EXTRA-ADRENAL SITE               1                31
[1] 2 2
[1] FALSE
D6V4, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED     1   2
  SHROOM4 WILD-TYPE 100  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      1    2
  SHROOM4 WILD-TYPE  100   76
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  FEMALE               1               100
  MALE                 2                76
[1] 2 2
[1] FALSE
D6V5, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED     3   0
  SHROOM4 WILD-TYPE 169   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      3    0
  SHROOM4 WILD-TYPE  169    5
     clus
vv    SHROOM4 MUTATED SHROOM4 WILD-TYPE
  NO                3               169
  YES               0                 5
[1] 2 2
[1] FALSE
D6V6, continuous
[1] "Remove cluster labels:" "SHROOM4 MUTATED"       
clus
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                1                61 
       TCGA-S7-A7WQ        TCGA-S7-A7WU        TCGA-S7-A7X1        TCGA-SR-A6MR 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-SR-A6MV        TCGA-WB-A817        TCGA-WB-A81E        TCGA-XG-A823 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-P7-A5NX        TCGA-P7-A5NY        TCGA-PR-A5PF        TCGA-PR-A5PG 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-PR-A5PH        TCGA-RT-A6YA        TCGA-RT-A6YC        TCGA-RX-A8JQ 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-S7-A7WL        TCGA-S7-A7WM        TCGA-S7-A7WO        TCGA-S7-A7WP 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-S7-A7WR        TCGA-S7-A7WT        TCGA-S7-A7WV        TCGA-S7-A7WW 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-S7-A7WX        TCGA-S7-A7X0        TCGA-S7-A7X2        TCGA-SP-A6QC 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-SP-A6QD        TCGA-SP-A6QF        TCGA-SP-A6QG        TCGA-SP-A6QI 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-SP-A6QJ        TCGA-SP-A6QK        TCGA-SR-A6MQ        TCGA-SR-A6MS 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-SR-A6MY        TCGA-SR-A6MZ        TCGA-SR-A6N0        TCGA-TT-A6YK 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-TT-A6YN        TCGA-TT-A6YO        TCGA-TT-A6YP        TCGA-WB-A80K 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A80L        TCGA-WB-A80Q        TCGA-WB-A815        TCGA-WB-A818 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A81D        TCGA-WB-A81F        TCGA-WB-A81G        TCGA-WB-A81H 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A81I        TCGA-WB-A81J        TCGA-WB-A81K        TCGA-WB-A81M 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A81N        TCGA-WB-A81S        TCGA-WB-A81T        TCGA-WB-A821 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-WB-A822 
"SHROOM4 WILD-TYPE" 
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  SHROOM4 MUTATED               0                                             1
  SHROOM4 WILD-TYPE            18                                            12
                   vv
clus                PHEOCHROMOCYTOMA
  SHROOM4 MUTATED                  2
  SHROOM4 WILD-TYPE              146
D6V7, multiclass
                                               clus
vv                                              SHROOM4 MUTATED
  PARAGANGLIOMA                                               0
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               1
  PHEOCHROMOCYTOMA                                            2
                                               clus
vv                                              SHROOM4 WILD-TYPE
  PARAGANGLIOMA                                                18
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                12
  PHEOCHROMOCYTOMA                                            146
[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
  SHROOM4 MUTATED                                  0     0
  SHROOM4 WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SHROOM4 MUTATED                           0     3
  SHROOM4 WILD-TYPE                        20   145
D6V9, multiclass
                                  clus
vv                                 SHROOM4 MUTATED SHROOM4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      0                20
  WHITE                                          3               145
[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"
D6V10, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED     1   1
  SHROOM4 WILD-TYPE   4 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      1    1
  SHROOM4 WILD-TYPE    4  137
                        clus
vv                       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               1               137
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMMECR1 MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  AMMECR1 MUTATED     3   0
  AMMECR1 WILD-TYPE 170   6
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                3               176 
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                0                 6 
$`AMMECR1 MUTATED`
TCGA-WB-A814 TCGA-P8-A6RX TCGA-RW-A688 
       74.04        17.75         1.22 

$`AMMECR1 WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A6ZZ TCGA-QR-A700 TCGA-QR-A703 
       58.88        30.51        14.17         1.58        32.15        38.37 
TCGA-QR-A705 TCGA-QR-A70D TCGA-QR-A70O TCGA-QR-A70P TCGA-QR-A70T TCGA-RW-A68A 
       10.42         0.23         3.65       117.14         8.78        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-SP-A6QH TCGA-SR-A6MR TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB 
       18.94        72.43        79.20       121.05         3.12        19.86 
TCGA-W2-A7HF TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 TCGA-XG-A823 
       17.69        43.07        48.53        24.82        10.16        20.19 
TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RY TCGA-PR-A5PF 
       26.89        31.46        29.03         4.04         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-A6GW TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 
       16.14        19.04         1.05         9.21         9.93        14.27 
TCGA-QR-A6H4 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 TCGA-QR-A707 
       87.48        31.53        15.58         1.28         4.11        13.08 
TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.15        69.67       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70M TCGA-QR-A70N TCGA-QR-A70Q 
       29.92        13.12         9.01        33.99         1.41         4.60 
TCGA-QR-A70R TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN 
       14.20        48.43         0.07        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-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       27.22         6.28        72.79        11.57         2.89        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR 
       31.59        36.56        37.25        35.51        31.04        40.70 
TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 
       42.77        27.91        23.21        25.32        17.95        24.20 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
        9.73       114.77       109.25        82.62        79.46       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       15.52       111.25         1.41         0.10        51.22        68.61 
TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
       81.93       106.75       110.53        24.66        26.20        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        37.35        19.92        13.32        42.48        20.09 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HH 
       17.16         1.18        14.43        18.44        16.60        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       14.79        41.26        34.26         4.47         4.73        25.51 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 
      316.73       127.56        29.16        19.59        53.59        41.23 
TCGA-WB-A818 TCGA-WB-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 

  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
             1.22              0.07 
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
            74.04            316.73 
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
           17.750            24.935 
[1] "1.2 - 74.0 (17.8)"  "0.1 - 316.7 (24.9)"
[1] "hr="     "9100000"
D7V2, continuous
D7V3, binary
                   cls
clus                  0   1
  AMMECR1 MUTATED     1   2
  AMMECR1 WILD-TYPE 146  30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMMECR1 MUTATED      1    2
  AMMECR1 WILD-TYPE  146   30
                    clus
vv                   AMMECR1 MUTATED AMMECR1 WILD-TYPE
  ADRENAL GLAND                    1               146
  EXTRA-ADRENAL SITE               2                30
[1] 2 2
[1] FALSE
D7V4, binary
                   cls
clus                 0  1
  AMMECR1 MUTATED    2  1
  AMMECR1 WILD-TYPE 99 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMMECR1 MUTATED      2    1
  AMMECR1 WILD-TYPE   99   77
        clus
vv       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  FEMALE               2                99
  MALE                 1                77
[1] 2 2
[1] FALSE
D7V5, binary
                   cls
clus                  0   1
  AMMECR1 MUTATED     3   0
  AMMECR1 WILD-TYPE 169   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMMECR1 MUTATED      3    0
  AMMECR1 WILD-TYPE  169    5
     clus
vv    AMMECR1 MUTATED AMMECR1 WILD-TYPE
  NO                3               169
  YES               0                 5
[1] 2 2
[1] FALSE
D7V6, continuous
                   vv
clus                PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  AMMECR1 MUTATED               1                                             1
  AMMECR1 WILD-TYPE            17                                            12
                   vv
clus                PHEOCHROMOCYTOMA
  AMMECR1 MUTATED                  1
  AMMECR1 WILD-TYPE              147
D7V7, multiclass
                                               clus
vv                                              AMMECR1 MUTATED
  PARAGANGLIOMA                                               1
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA               1
  PHEOCHROMOCYTOMA                                            1
                                               clus
vv                                              AMMECR1 WILD-TYPE
  PARAGANGLIOMA                                                17
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA                12
  PHEOCHROMOCYTOMA                                            147
[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
[1] "Remove cluster labels:" "AMMECR1 MUTATED"       
clus
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                1                20 
       TCGA-QR-A705        TCGA-QR-A70D        TCGA-QR-A70P        TCGA-QR-A70T 
"AMMECR1 WILD-TYPE" "AMMECR1 WILD-TYPE" "AMMECR1 WILD-TYPE" "AMMECR1 WILD-TYPE" 
       TCGA-SR-A6MR        TCGA-WB-A820        TCGA-XG-A823        TCGA-PR-A5PG 
"AMMECR1 WILD-TYPE" "AMMECR1 WILD-TYPE" "AMMECR1 WILD-TYPE" "AMMECR1 WILD-TYPE" 
       TCGA-PR-A5PH        TCGA-QR-A702        TCGA-QT-A5XJ        TCGA-QT-A5XP 
"AMMECR1 WILD-TYPE" "AMMECR1 WILD-TYPE" "AMMECR1 WILD-TYPE" "AMMECR1 WILD-TYPE" 
       TCGA-QT-A69Q        TCGA-RW-A680        TCGA-RW-A686        TCGA-RW-A8AZ 
"AMMECR1 WILD-TYPE" "AMMECR1 WILD-TYPE" "AMMECR1 WILD-TYPE" "AMMECR1 WILD-TYPE" 
       TCGA-TT-A6YK        TCGA-WB-A80Q        TCGA-WB-A80Y        TCGA-WB-A81W 
"AMMECR1 WILD-TYPE" "AMMECR1 WILD-TYPE" "AMMECR1 WILD-TYPE" "AMMECR1 WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMMECR1 MUTATED                                  0     0
  AMMECR1 WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  AMMECR1 MUTATED                           1     2
  AMMECR1 WILD-TYPE                        19   146
D7V9, multiclass
                                  clus
vv                                 AMMECR1 MUTATED AMMECR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      1                19
  WHITE                                          2               146
[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"
D7V10, binary
                   cls
clus                  0   1
  AMMECR1 MUTATED     0   2
  AMMECR1 WILD-TYPE   5 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMMECR1 MUTATED      0    2
  AMMECR1 WILD-TYPE    5  136
                        clus
vv                       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               2               136
[1] 2 2
[1] FALSE

Clustering(8) Variable = GPR128 MUTATION ANALYSIS
D8V1, survival
                  sevent
clus2                0   1
  GPR128 MUTATED     4   0
  GPR128 WILD-TYPE 169   6
  GPR128 MUTATED GPR128 WILD-TYPE 
               4              175 
  GPR128 MUTATED GPR128 WILD-TYPE 
               0                6 
$`GPR128 MUTATED`
TCGA-P7-A5NY TCGA-QR-A70A TCGA-QR-A7IN TCGA-W2-A7H7 
       31.46        69.67        12.39        17.16 

$`GPR128 WILD-TYPE`
TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H1 TCGA-QR-A6ZZ TCGA-QR-A700 TCGA-QR-A703 
       58.88        30.51        14.17         1.58        32.15        38.37 
TCGA-QR-A705 TCGA-QR-A70D TCGA-QR-A70O TCGA-QR-A70P TCGA-QR-A70T TCGA-RW-A68A 
       10.42         0.23         3.65       117.14         8.78        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-SP-A6QH TCGA-SR-A6MR TCGA-SR-A6MV TCGA-SR-A6MX TCGA-W2-A7HB 
       18.94        72.43        79.20       121.05         3.12        19.86 
TCGA-W2-A7HF TCGA-WB-A814 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81Q TCGA-WB-A820 
       17.69        74.04        43.07        48.53        24.82        10.16 
TCGA-XG-A823 TCGA-P7-A5NX TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY 
       20.19        26.89        29.03         4.04        17.75         5.88 
TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS 
       17.95        81.70        28.08        35.01        23.11         1.25 
TCGA-QR-A6GT TCGA-QR-A6GW TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6H0 TCGA-QR-A6H2 
      137.59        16.14        19.04         1.05         9.21         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H4 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A702 TCGA-QR-A706 
       14.27        87.48        31.53        15.58         1.28         4.11 
TCGA-QR-A707 TCGA-QR-A708 TCGA-QR-A70C TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
       13.08         1.15       116.19         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70M TCGA-QR-A70N TCGA-QR-A70Q 
       29.92        13.12         9.01        33.99         1.41         4.60 
TCGA-QR-A70R TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IP 
       14.20        48.43         0.07        41.79         6.02        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       36.23         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        4.41         0.79        13.08        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       50.63         8.09        86.89        19.86         2.93         7.10 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
       47.64        37.51         1.05         0.85        19.30         1.22 
TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       27.22         6.28        72.79        11.57         2.89        20.09 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR 
       31.59        36.56        37.25        35.51        31.04        40.70 
TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 
       42.77        27.91        23.21        25.32        17.95        24.20 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
        9.73       114.77       109.25        82.62        79.46       110.04 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       15.52       111.25         1.41         0.10        51.22        68.61 
TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
       81.93       106.75       110.53        24.66        26.20        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        37.35        19.92        13.32        42.48        20.09 
TCGA-W2-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-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 
        1.61        23.77        25.51        71.05        78.21        93.11 
TCGA-WB-A822 
      103.17 

  GPR128 MUTATED GPR128 WILD-TYPE 
           12.39             0.07 
  GPR128 MUTATED GPR128 WILD-TYPE 
           69.67           316.73 
  GPR128 MUTATED GPR128 WILD-TYPE 
           24.31            24.82 
[1] "12.4 - 69.7 (24.3)" "0.1 - 316.7 (24.8)"
[1] "hr="     "9200000"
D8V2, continuous
D8V3, binary
                  cls
clus                 0   1
  GPR128 MUTATED     4   0
  GPR128 WILD-TYPE 143  32
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR128 MUTATED      4    0
  GPR128 WILD-TYPE  143   32
                    clus
vv                   GPR128 MUTATED GPR128 WILD-TYPE
  ADRENAL GLAND                   4              143
  EXTRA-ADRENAL SITE              0               32
[1] 2 2
[1] FALSE
D8V4, binary
                  cls
clus                0  1
  GPR128 MUTATED    3  1
  GPR128 WILD-TYPE 98 77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR128 MUTATED      3    1
  GPR128 WILD-TYPE   98   77
        clus
vv       GPR128 MUTATED GPR128 WILD-TYPE
  FEMALE              3               98
  MALE                1               77
[1] 2 2
[1] FALSE
D8V5, binary
                  cls
clus                 0   1
  GPR128 MUTATED     4   0
  GPR128 WILD-TYPE 168   5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR128 MUTATED      4    0
  GPR128 WILD-TYPE  168    5
     clus
vv    GPR128 MUTATED GPR128 WILD-TYPE
  NO               4              168
  YES              0                5
[1] 2 2
[1] FALSE
D8V6, continuous
[1] "Remove cluster labels:" "GPR128 MUTATED"        
clus
  GPR128 MUTATED GPR128 WILD-TYPE 
               1               61 
      TCGA-S7-A7WQ       TCGA-S7-A7WU       TCGA-S7-A7X1       TCGA-SR-A6MR 
"GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" 
      TCGA-SR-A6MV       TCGA-WB-A817       TCGA-WB-A81E       TCGA-XG-A823 
"GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" 
      TCGA-P7-A5NX       TCGA-PR-A5PF       TCGA-PR-A5PG       TCGA-PR-A5PH 
"GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" 
      TCGA-RT-A6YA       TCGA-RT-A6YC       TCGA-RX-A8JQ       TCGA-S7-A7WL 
"GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" 
      TCGA-S7-A7WM       TCGA-S7-A7WN       TCGA-S7-A7WO       TCGA-S7-A7WP 
"GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" 
      TCGA-S7-A7WR       TCGA-S7-A7WT       TCGA-S7-A7WV       TCGA-S7-A7WW 
"GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" 
      TCGA-S7-A7WX       TCGA-S7-A7X0       TCGA-S7-A7X2       TCGA-SP-A6QC 
"GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" 
      TCGA-SP-A6QD       TCGA-SP-A6QF       TCGA-SP-A6QG       TCGA-SP-A6QI 
"GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" 
      TCGA-SP-A6QJ       TCGA-SP-A6QK       TCGA-SR-A6MQ       TCGA-SR-A6MS 
"GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" 
      TCGA-SR-A6MY       TCGA-SR-A6MZ       TCGA-SR-A6N0       TCGA-TT-A6YK 
"GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" 
      TCGA-TT-A6YN       TCGA-TT-A6YO       TCGA-TT-A6YP       TCGA-WB-A80K 
"GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" 
      TCGA-WB-A80L       TCGA-WB-A80Q       TCGA-WB-A815       TCGA-WB-A818 
"GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" 
      TCGA-WB-A81D       TCGA-WB-A81F       TCGA-WB-A81G       TCGA-WB-A81H 
"GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" 
      TCGA-WB-A81I       TCGA-WB-A81J       TCGA-WB-A81K       TCGA-WB-A81M 
"GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" 
      TCGA-WB-A81N       TCGA-WB-A81S       TCGA-WB-A81T       TCGA-WB-A821 
"GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" "GPR128 WILD-TYPE" 
      TCGA-WB-A822 
"GPR128 WILD-TYPE" 
                  vv
clus               PARAGANGLIOMA PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA
  GPR128 MUTATED               0                                             0
  GPR128 WILD-TYPE            18                                            13
                  vv
clus               PHEOCHROMOCYTOMA
  GPR128 MUTATED                  4
  GPR128 WILD-TYPE              144
D8V7, multiclass
                                               clus
vv                                              GPR128 MUTATED GPR128 WILD-TYPE
  PARAGANGLIOMA                                              0               18
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA              0               13
  PHEOCHROMOCYTOMA                                           4              144
[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
  GPR128 MUTATED                                  0     0
  GPR128 WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR128 MUTATED                           1     3
  GPR128 WILD-TYPE                        19   145
D8V9, multiclass
                                  clus
vv                                 GPR128 MUTATED GPR128 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                6
  BLACK OR AFRICAN AMERICAN                     1               19
  WHITE                                         3              145
[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"
D8V10, binary
                  cls
clus                 0   1
  GPR128 MUTATED     0   4
  GPR128 WILD-TYPE   5 134
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR128 MUTATED      0    4
  GPR128 WILD-TYPE    5  134
                        clus
vv                       GPR128 MUTATED GPR128 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4              134
[1] 2 2
[1] FALSE
