[1] "ofn"        "-oTPCPG-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PCPG-TP/15087180/PCPG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PCPG-TP/15165019/transformed.cor.cli.txt"

nPatients in clinical file=179, in cluster file=178, common to both=178
[1]   9 178
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            18            160 
  HRAS MUTATED HRAS WILD-TYPE 
            18            160 
[1] "EPAS1 MUTATION ANALYSIS"
[1] 3
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              8             170 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              8             170 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           15           163 
  NF1 MUTATED NF1 WILD-TYPE 
           15           163 
[1] "RET MUTATION ANALYSIS"
[1] 3
  RET MUTATED RET WILD-TYPE 
            6           172 
  RET MUTATED RET WILD-TYPE 
            6           172 
[1] "CSDE1 MUTATION ANALYSIS"
[1] 3
  CSDE1 MUTATED CSDE1 WILD-TYPE 
              4             174 
  CSDE1 MUTATED CSDE1 WILD-TYPE 
              4             174 
[1] "GPR128 MUTATION ANALYSIS"
[1] 3
  GPR128 MUTATED GPR128 WILD-TYPE 
               4              174 
  GPR128 MUTATED GPR128 WILD-TYPE 
               4              174 
[1] "AMMECR1 MUTATION ANALYSIS"
[1] 3
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                3               175 
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                3               175 
[1] "SHROOM4 MUTATION ANALYSIS"
[1] 3
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                3               175 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                3               175 
[1] "FAM83D MUTATION ANALYSIS"
[1] 3
  FAM83D MUTATED FAM83D WILD-TYPE 
               3              175 
  FAM83D MUTATED FAM83D WILD-TYPE 
               3              175 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "DCC_UPLOAD_DATE"                       
 [6] "GENDER"                                
 [7] "RADIATION_THERAPY"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[11] "BATCH_NUMBER"                          

Input Data has 11 rows and 178 columns.

[1] "Batch" "11"   
[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=162,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'BATCH_NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 178 columns, 1 survival variables, and 4 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH" "GENDER"         "RACE"           "ETHNICITY"     
YEARS_TO_BIRTH, nv=59, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
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 154   6
  HRAS MUTATED HRAS WILD-TYPE 
            18            160 
  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 
        2.27        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 
       12.03        12.49         4.73         4.21         1.61        18.28 

$`HRAS WILD-TYPE`
TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       26.89        31.46        29.03        17.75         5.88        17.95 
TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GU 
       28.08        35.01        23.11         1.25       137.59        58.88 
TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 
       19.04         1.05        30.51         9.21        14.17         9.93 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A6ZZ TCGA-QR-A702 TCGA-QR-A703 
       14.27        31.53        15.58         1.58         1.28        38.37 
TCGA-QR-A705 TCGA-QR-A706 TCGA-QR-A707 TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C 
       10.42         4.11        13.08         1.15        69.67       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J 
        0.23         6.31         2.33        26.83        29.92        13.12 
TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70O TCGA-QR-A70P TCGA-QR-A70Q TCGA-QR-A70R 
        9.01         1.41         3.65       117.14         4.60        14.20 
TCGA-QR-A70T TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
        8.78        48.43         0.07         6.02        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       36.23         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        4.41         0.79        13.08        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       50.63         8.09        86.89        19.86         2.93         7.10 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
       33.30        23.80         1.05         0.85        13.32         1.22 
TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F 
       11.70        13.05         7.96         6.28        72.79        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
       41.88         4.41         1.78         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WT TCGA-S7-A7WU 
       30.21        35.51        31.04        26.96        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       27.91        20.58        25.32        12.66        18.94        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QH TCGA-SP-A6QI 
        9.73       114.77       109.25        67.50        72.43       110.04 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MR TCGA-SR-A6MS 
      111.25         1.41         0.10        51.22        79.20        81.93 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MZ TCGA-SR-A6N0 
      106.75       110.53       121.05         3.12        19.76        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        25.15        19.92        13.32        25.32        14.20 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       17.16         1.18        19.86        16.60        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80P TCGA-WB-A80Q 
       10.65        34.82        34.26         4.47       316.73       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 
       29.16        19.59        32.88         5.98        41.23        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       34.03        33.90        24.16        35.84        37.18        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        42.54        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81S TCGA-WB-A81V TCGA-WB-A81W 
       53.69        12.99        24.82        23.77        71.05        78.21 
TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       10.16        93.11       103.17        20.19 

  HRAS MUTATED HRAS WILD-TYPE 
          1.61           0.07 
  HRAS MUTATED HRAS WILD-TYPE 
         87.48         316.73 
  HRAS MUTATED HRAS WILD-TYPE 
        21.470         20.385 
[1] "1.6 - 87.5 (21.5)"  "0.1 - 316.7 (20.4)"
[1] "hr="     "7.8e+07"
D1V2, continuous
D1V3, binary
                cls
clus              0  1
  HRAS MUTATED   11  7
  HRAS WILD-TYPE 90 70
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED     11    7
  HRAS WILD-TYPE   90   70
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  FEMALE           11             90
  MALE              7             70
[1] 2 2
[1] FALSE
                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   131
D1V4, 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            131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                cls
clus               0   1
  HRAS MUTATED     0  17
  HRAS WILD-TYPE   5 120
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0   17
  HRAS WILD-TYPE    5  120
                        clus
vv                       HRAS MUTATED HRAS WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO           17            120
[1] 2 2
[1] FALSE

Clustering(2) Variable = EPAS1 MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2               0   1
  EPAS1 MUTATED     8   0
  EPAS1 WILD-TYPE 164   6
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              8             170 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              0               6 
$`EPAS1 MUTATED`
TCGA-QR-A7IN TCGA-QT-A5XL TCGA-QT-A7U0 TCGA-RW-A68D TCGA-S7-A7X0 TCGA-SR-A6MV 
       12.39         1.81        13.08        72.79        12.66       121.05 
TCGA-WB-A814 TCGA-WB-A821 
       32.88        93.11 

$`EPAS1 WILD-TYPE`
TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY 
       26.89        31.46        29.03         2.27        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-A6GU TCGA-QR-A6GW TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ 
      137.59        58.88        16.14        19.04         1.05        30.51 
TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H4 TCGA-QR-A6H5 
        9.21        14.17         9.93        14.27        87.48        31.53 
TCGA-QR-A6H6 TCGA-QR-A6ZZ TCGA-QR-A702 TCGA-QR-A703 TCGA-QR-A705 TCGA-QR-A706 
       15.58         1.58         1.28        38.37        10.42         4.11 
TCGA-QR-A707 TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E 
       13.08         1.15        69.67       116.19         0.23         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-A70O TCGA-QR-A70P TCGA-QR-A70Q TCGA-QR-A70R TCGA-QR-A70T 
        1.41         3.65       117.14         4.60        14.20         8.78 
TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IP TCGA-QT-A5XJ 
       48.43         0.07        41.79         6.02        17.95        36.23 
TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q 
        6.94         0.72        25.18         2.30         4.41         0.79 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       77.98         0.92       108.26        50.63         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       19.86         2.93         7.10        33.30        23.80         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        0.85        13.32         1.22        11.70        13.05         7.96 
TCGA-RW-A68C TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
        6.28        15.02        41.88         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
       20.09        31.59        30.21        37.25        35.51        31.04 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       26.96        40.70        37.58        30.51        27.91        20.58 
TCGA-S7-A7WX TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       25.32        18.94        18.08         9.73       114.77       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QH TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
       82.62        67.50        72.43       110.04        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MR TCGA-SR-A6MS 
        1.41         0.10        51.22        68.61        79.20        81.93 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
      106.75       110.53         3.12        24.66        19.76        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        25.15        19.92        13.32        25.32        14.20 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       17.16         1.18        19.86        12.03        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       17.69        25.61        10.65        34.82        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       316.73       127.56        29.16        19.59 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A 
        5.98        41.23        32.61        34.03        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
       24.36        40.04        45.83        53.69        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
        1.61        23.77        18.28        71.05        78.21        10.16 
TCGA-WB-A822 TCGA-XG-A823 
      103.17        20.19 

  EPAS1 MUTATED EPAS1 WILD-TYPE 
           1.81            0.07 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
         121.05          316.73 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
         22.980          20.385 
[1] "1.8 - 121.0 (23.0)" "0.1 - 316.7 (20.4)"
[1] "hr="     "8.1e+07"
D2V2, continuous
D2V3, binary
                 cls
clus               0  1
  EPAS1 MUTATED    6  2
  EPAS1 WILD-TYPE 95 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPAS1 MUTATED      6    2
  EPAS1 WILD-TYPE   95   75
        clus
vv       EPAS1 MUTATED EPAS1 WILD-TYPE
  FEMALE             6              95
  MALE               2              75
[1] 2 2
[1] FALSE
                 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   142
D2V4, 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             142
[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"
D2V5, binary
                 cls
clus                0   1
  EPAS1 MUTATED     0   6
  EPAS1 WILD-TYPE   5 131
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPAS1 MUTATED      0    6
  EPAS1 WILD-TYPE    5  131
                        clus
vv                       EPAS1 MUTATED EPAS1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6             131
[1] 2 2
[1] FALSE

Clustering(3) Variable = NF1 MUTATION ANALYSIS
D3V1, survival
               sevent
clus2             0   1
  NF1 MUTATED    15   0
  NF1 WILD-TYPE 157   6
  NF1 MUTATED NF1 WILD-TYPE 
           15           163 
  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        11.70         1.78        31.59        30.21         0.10 
TCGA-WB-A818 TCGA-WB-A81P TCGA-WB-A81V 
       34.03        12.99        71.05 

$`NF1 WILD-TYPE`
TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY 
       26.89        31.46        29.03         2.27        17.75         5.88 
TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GT 
       17.95        81.70        28.08        35.01        23.11       137.59 
TCGA-QR-A6GU TCGA-QR-A6GW TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 
       58.88        16.14        19.04         1.05        30.51         9.21 
TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H4 TCGA-QR-A6H5 TCGA-QR-A6H6 
       14.17         9.93        14.27        87.48        31.53        15.58 
TCGA-QR-A6ZZ TCGA-QR-A703 TCGA-QR-A705 TCGA-QR-A706 TCGA-QR-A707 TCGA-QR-A708 
        1.58        38.37        10.42         4.11        13.08         1.15 
TCGA-QR-A70A TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
       69.67       116.19         0.23         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70M TCGA-QR-A70N TCGA-QR-A70O 
       29.92        13.12         9.01        33.99         1.41         3.65 
TCGA-QR-A70P TCGA-QR-A70Q TCGA-QR-A70R TCGA-QR-A70T TCGA-QR-A70U TCGA-QR-A70W 
      117.14         4.60        14.20         8.78        48.43        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-A6YC TCGA-RW-A67V TCGA-RW-A67W 
       77.98         0.92       108.26         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A686 TCGA-RW-A68A 
        2.93        33.30        23.80         1.05        13.32        13.05 
TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
        7.96         6.28        72.79        15.02        41.88         4.41 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
        2.89        20.09        37.25        35.51        31.04        26.96 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       40.70        37.58        30.51        27.91        20.58        25.32 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD 
       12.66        18.94        18.08         9.73       114.77       109.25 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QH TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
       82.62        67.50        72.43       110.04        15.52       111.25 
TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MR TCGA-SR-A6MS TCGA-SR-A6MT 
        1.41        51.22        68.61        79.20        81.93       106.75 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
      110.53       121.05         3.12        24.66        19.76        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        25.15        19.92        13.32        25.32        14.20 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       17.16         1.18        19.86        12.03        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       17.69        25.61        10.65        34.82        34.26         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       316.73       127.56        29.16        19.59 
TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A819 TCGA-WB-A81A 
       32.88         5.98        41.23        32.61        33.90        24.16 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
       35.84        37.18        57.11        38.76        42.54        22.32 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81Q TCGA-WB-A81R 
       24.36        40.04        45.83        53.69        24.82         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 
       23.77        18.28        78.21        10.16        93.11       103.17 
TCGA-XG-A823 
       20.19 

  NF1 MUTATED NF1 WILD-TYPE 
         0.07          0.23 
  NF1 MUTATED NF1 WILD-TYPE 
        71.05        316.73 
  NF1 MUTATED NF1 WILD-TYPE 
         7.10         23.11 
[1] "0.1 - 71.0 (7.1)"   "0.2 - 316.7 (23.1)"
[1] "hr="     "2.6e+07"
D3V2, continuous
D3V3, binary
               cls
clus             0  1
  NF1 MUTATED    9  6
  NF1 WILD-TYPE 92 71
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      9    6
  NF1 WILD-TYPE   92   71
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE           9            92
  MALE             6            71
[1] 2 2
[1] FALSE
               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   133
D3V4, 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           133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
               cls
clus              0   1
  NF1 MUTATED     1   8
  NF1 WILD-TYPE   4 129
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      1    8
  NF1 WILD-TYPE    4  129
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               1             4
  NOT HISPANIC OR LATINO           8           129
[1] 2 2
[1] FALSE

Clustering(4) Variable = RET MUTATION ANALYSIS
D4V1, survival
               sevent
clus2             0   1
  RET MUTATED     6   0
  RET WILD-TYPE 166   6
  RET MUTATED RET WILD-TYPE 
            6           172 
  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-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY 
       26.89        31.46        29.03         2.27        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-A6GU TCGA-QR-A6GW TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ 
      137.59        58.88        16.14        19.04         1.05        30.51 
TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H4 TCGA-QR-A6H5 
        9.21        14.17         9.93        14.27        87.48        31.53 
TCGA-QR-A6H6 TCGA-QR-A6ZZ TCGA-QR-A702 TCGA-QR-A703 TCGA-QR-A705 TCGA-QR-A706 
       15.58         1.58         1.28        38.37        10.42         4.11 
TCGA-QR-A707 TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E 
       13.08         1.15        69.67       116.19         0.23         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-A70O TCGA-QR-A70P TCGA-QR-A70Q TCGA-QR-A70R TCGA-QR-A70T 
        1.41         3.65       117.14         4.60        14.20         8.78 
TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
       48.43         0.07        41.79         6.02        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q 
       36.23         1.81        25.18         2.30         4.41         0.79 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC 
       13.08        77.98         0.92       108.26        50.63         8.09 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 
       86.89        19.86         2.93         7.10        33.30        23.80 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
        1.05         0.85        13.32         1.22        11.70        13.05 
TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
        7.96         6.28        72.79        15.02        41.88         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89        20.09        31.59        30.21        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       35.51        31.04        26.96        40.70        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       27.91        20.58        25.32        12.66        18.94        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QH 
        9.73       114.77       109.25        82.62        67.50        72.43 
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-A6MR TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX 
       79.20        81.93       106.75       110.53       121.05         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        19.76        49.61         4.34        25.15        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HB TCGA-W2-A7HC 
       13.32        25.32        14.20        17.16        19.86        12.03 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       12.49        16.60        17.69        25.61        10.65        34.82 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       34.26         4.47         4.73         4.21       316.73       127.56 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 
       19.59        32.88         5.98        41.23        32.61        34.03 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       24.16        35.84        37.18        57.11        38.76        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       22.32        24.36        40.04        45.83        53.69        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        23.77        18.28        71.05        78.21 
TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       10.16        93.11       103.17        20.19 

  RET MUTATED RET WILD-TYPE 
         0.72          0.07 
  RET MUTATED RET WILD-TYPE 
       111.25        316.73 
  RET MUTATED RET WILD-TYPE 
       18.050        20.385 
[1] "0.7 - 111.2 (18.1)" "0.1 - 316.7 (20.4)"
[1] "hr="     "2.5e+07"
D4V2, continuous
D4V3, binary
               cls
clus             0  1
  RET MUTATED    4  2
  RET WILD-TYPE 97 75
[1] "tbl2"
               cls
clus            [,1] [,2]
  RET MUTATED      4    2
  RET WILD-TYPE   97   75
        clus
vv       RET MUTATED RET WILD-TYPE
  FEMALE           4            97
  MALE             2            75
[1] 2 2
[1] FALSE
               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   144
D4V4, 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           144
[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"
D4V5, binary
               cls
clus              0   1
  RET MUTATED     0   4
  RET WILD-TYPE   5 133
[1] "tbl2"
               cls
clus            [,1] [,2]
  RET MUTATED      0    4
  RET WILD-TYPE    5  133
                        clus
vv                       RET MUTATED RET WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           4           133
[1] 2 2
[1] FALSE

Clustering(5) Variable = CSDE1 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  CSDE1 MUTATED     4   0
  CSDE1 WILD-TYPE 168   6
  CSDE1 MUTATED CSDE1 WILD-TYPE 
              4             174 
  CSDE1 MUTATED CSDE1 WILD-TYPE 
              0               6 
$`CSDE1 MUTATED`
TCGA-RW-A681 TCGA-S7-A7WT TCGA-WB-A80M TCGA-WB-A81M 
       23.80        37.58         4.47        45.83 

$`CSDE1 WILD-TYPE`
TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY 
       26.89        31.46        29.03         2.27        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-A6GU TCGA-QR-A6GW TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ 
      137.59        58.88        16.14        19.04         1.05        30.51 
TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H4 TCGA-QR-A6H5 
        9.21        14.17         9.93        14.27        87.48        31.53 
TCGA-QR-A6H6 TCGA-QR-A6ZZ TCGA-QR-A702 TCGA-QR-A703 TCGA-QR-A705 TCGA-QR-A706 
       15.58         1.58         1.28        38.37        10.42         4.11 
TCGA-QR-A707 TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E 
       13.08         1.15        69.67       116.19         0.23         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-A70O TCGA-QR-A70P TCGA-QR-A70Q TCGA-QR-A70R TCGA-QR-A70T 
        1.41         3.65       117.14         4.60        14.20         8.78 
TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
       48.43         0.07        41.79         6.02        12.39        17.95 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO 
       36.23         6.94         1.81         0.72        25.18         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        4.41         0.79        13.08        77.98         0.92       108.26 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       50.63         8.09        86.89        19.86         2.93         7.10 
TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 
       33.30         1.05         0.85        13.32         1.22        11.70 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G 
       13.05         7.96         6.28        72.79        15.02        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89        20.09        31.59        30.21 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WU 
       37.25        35.51        31.04        26.96        40.70        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       27.91        20.58        25.32        12.66        18.94        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QH 
        9.73       114.77       109.25        82.62        67.50        72.43 
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-A6MR TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
       68.61        79.20        81.93       106.75       110.53       121.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        19.76        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       19.92        13.32        25.32        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       19.86        12.03        12.49        16.60        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
       10.65        34.82        34.26         4.73         4.21       316.73 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 
      127.56        29.16        19.59        32.88         5.98        41.23 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        34.03        33.90        24.16        35.84        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       57.11        38.76        42.54        22.32        24.36        40.04 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       53.69        12.99        24.82         1.61        23.77        18.28 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        78.21        10.16        93.11       103.17        20.19 

  CSDE1 MUTATED CSDE1 WILD-TYPE 
           4.47            0.07 
  CSDE1 MUTATED CSDE1 WILD-TYPE 
          45.83          316.73 
  CSDE1 MUTATED CSDE1 WILD-TYPE 
          30.69           20.14 
[1] "4.5 - 45.8 (30.7)"  "0.1 - 316.7 (20.1)"
[1] "hr="     "9300000"
D5V2, continuous
D5V3, binary
                 cls
clus                0   1
  CSDE1 MUTATED     1   3
  CSDE1 WILD-TYPE 100  74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSDE1 MUTATED      1    3
  CSDE1 WILD-TYPE  100   74
        clus
vv       CSDE1 MUTATED CSDE1 WILD-TYPE
  FEMALE             1             100
  MALE               3              74
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSDE1 MUTATED                                  0     0
  CSDE1 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CSDE1 MUTATED                           0     4
  CSDE1 WILD-TYPE                        20   143
D5V4, multiclass
                                  clus
vv                                 CSDE1 MUTATED CSDE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               6
  BLACK OR AFRICAN AMERICAN                    0              20
  WHITE                                        4             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"
D5V5, binary
                 cls
clus                0   1
  CSDE1 MUTATED     0   2
  CSDE1 WILD-TYPE   5 135
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSDE1 MUTATED      0    2
  CSDE1 WILD-TYPE    5  135
                        clus
vv                       CSDE1 MUTATED CSDE1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2             135
[1] 2 2
[1] FALSE

Clustering(6) Variable = GPR128 MUTATION ANALYSIS
D6V1, survival
                  sevent
clus2                0   1
  GPR128 MUTATED     4   0
  GPR128 WILD-TYPE 168   6
  GPR128 MUTATED GPR128 WILD-TYPE 
               4              174 
  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-P7-A5NX TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       26.89        29.03         2.27        17.75         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GW TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 
       58.88        16.14        19.04         1.05        30.51         9.21 
TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H4 TCGA-QR-A6H5 TCGA-QR-A6H6 
       14.17         9.93        14.27        87.48        31.53        15.58 
TCGA-QR-A6ZZ TCGA-QR-A702 TCGA-QR-A703 TCGA-QR-A705 TCGA-QR-A706 TCGA-QR-A707 
        1.58         1.28        38.37        10.42         4.11        13.08 
TCGA-QR-A708 TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G TCGA-QR-A70H 
        1.15       116.19         0.23         6.31         2.33        26.83 
TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70M TCGA-QR-A70N TCGA-QR-A70O 
       29.92        13.12         9.01        33.99         1.41         3.65 
TCGA-QR-A70P TCGA-QR-A70Q TCGA-QR-A70R TCGA-QR-A70T TCGA-QR-A70U TCGA-QR-A70V 
      117.14         4.60        14.20         8.78        48.43         0.07 
TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       41.79         6.02        17.95        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       77.98         0.92       108.26        50.63         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       19.86         2.93         7.10        33.30        23.80         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        0.85        13.32         1.22        11.70        13.05         7.96 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 
        6.28        72.79        15.02        41.88         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89        20.09        31.59        30.21        37.25        35.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       31.04        26.96        40.70        37.58        30.51        27.91 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SA-A6C2 
       20.58        25.32        12.66        18.94        18.08         9.73 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QH TCGA-SP-A6QI 
      114.77       109.25        82.62        67.50        72.43       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-A6MR TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX 
       79.20        81.93       106.75       110.53       121.05         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        19.76        49.61         4.34        25.15        19.92 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC 
       13.32        25.32        14.20         1.18        19.86        12.03 
TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       12.49        16.60        17.69        25.61        10.65        34.82 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       34.26         4.47         4.73         4.21       316.73       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 
       29.16        19.59        32.88         5.98        41.23        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       34.03        33.90        24.16        35.84        37.18        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       38.76        42.54        22.32        24.36        40.04        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       53.69        12.99        24.82         1.61        23.77        18.28 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        78.21        10.16        93.11       103.17        20.19 

  GPR128 MUTATED GPR128 WILD-TYPE 
           12.39             0.07 
  GPR128 MUTATED GPR128 WILD-TYPE 
           69.67           316.73 
  GPR128 MUTATED GPR128 WILD-TYPE 
          24.310           20.385 
[1] "12.4 - 69.7 (24.3)" "0.1 - 316.7 (20.4)"
[1] "hr="     "9300000"
D6V2, continuous
D6V3, binary
                  cls
clus                0  1
  GPR128 MUTATED    3  1
  GPR128 WILD-TYPE 98 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR128 MUTATED      3    1
  GPR128 WILD-TYPE   98   76
        clus
vv       GPR128 MUTATED GPR128 WILD-TYPE
  FEMALE              3               98
  MALE                1               76
[1] 2 2
[1] FALSE
                  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   144
D6V4, 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              144
[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"
D6V5, binary
                  cls
clus                 0   1
  GPR128 MUTATED     0   4
  GPR128 WILD-TYPE   5 133
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR128 MUTATED      0    4
  GPR128 WILD-TYPE    5  133
                        clus
vv                       GPR128 MUTATED GPR128 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4              133
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMMECR1 MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  AMMECR1 MUTATED     3   0
  AMMECR1 WILD-TYPE 169   6
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                3               175 
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                0                 6 
$`AMMECR1 MUTATED`
TCGA-P8-A6RX TCGA-RW-A688 TCGA-WB-A814 
       17.75         1.22        32.88 

$`AMMECR1 WILD-TYPE`
TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RY TCGA-PR-A5PF 
       26.89        31.46        29.03         2.27         5.88        17.95 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT 
       81.70        28.08        35.01        23.11         1.25       137.59 
TCGA-QR-A6GU TCGA-QR-A6GW TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H0 
       58.88        16.14        19.04         1.05        30.51         9.21 
TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H4 TCGA-QR-A6H5 TCGA-QR-A6H6 
       14.17         9.93        14.27        87.48        31.53        15.58 
TCGA-QR-A6ZZ TCGA-QR-A702 TCGA-QR-A703 TCGA-QR-A705 TCGA-QR-A706 TCGA-QR-A707 
        1.58         1.28        38.37        10.42         4.11        13.08 
TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70G 
        1.15        69.67       116.19         0.23         6.31         2.33 
TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70M TCGA-QR-A70N 
       26.83        29.92        13.12         9.01        33.99         1.41 
TCGA-QR-A70O TCGA-QR-A70P TCGA-QR-A70Q TCGA-QR-A70R TCGA-QR-A70T TCGA-QR-A70U 
        3.65       117.14         4.60        14.20         8.78        48.43 
TCGA-QR-A70V TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ 
        0.07        41.79         6.02        12.39        17.95        36.23 
TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP 
        6.94         1.81         0.72        25.18         2.30         4.41 
TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA 
        0.79        13.08        77.98         0.92       108.26        50.63 
TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 
        8.09        86.89        19.86         2.93         7.10        33.30 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A689 TCGA-RW-A68A 
       23.80         1.05         0.85        13.32        11.70        13.05 
TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
        7.96         6.28        72.79        15.02        41.88         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89        20.09        31.59        30.21        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       35.51        31.04        26.96        40.70        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       27.91        20.58        25.32        12.66        18.94        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QH 
        9.73       114.77       109.25        82.62        67.50        72.43 
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-A6MR TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
       68.61        79.20        81.93       106.75       110.53       121.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        19.76        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       19.92        13.32        25.32        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       19.86        12.03        12.49        16.60        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       10.65        34.82        34.26         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 
      316.73       127.56        29.16        19.59         5.98        41.23 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        34.03        33.90        24.16        35.84        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       57.11        38.76        42.54        22.32        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       45.83        53.69        12.99        24.82         1.61        23.77 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 
       18.28        71.05        78.21        10.16        93.11       103.17 
TCGA-XG-A823 
       20.19 

  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
             1.22              0.07 
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
            32.88            316.73 
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
            17.75             20.58 
[1] "1.2 - 32.9 (17.8)"  "0.1 - 316.7 (20.6)"
[1] "hr="     "9100000"
D7V2, continuous
D7V3, binary
                   cls
clus                 0  1
  AMMECR1 MUTATED    2  1
  AMMECR1 WILD-TYPE 99 76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMMECR1 MUTATED      2    1
  AMMECR1 WILD-TYPE   99   76
        clus
vv       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  FEMALE               2                99
  MALE                 1                76
[1] 2 2
[1] FALSE
                   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   145
D7V4, 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               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"
D7V5, binary
                   cls
clus                  0   1
  AMMECR1 MUTATED     0   2
  AMMECR1 WILD-TYPE   5 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMMECR1 MUTATED      0    2
  AMMECR1 WILD-TYPE    5  135
                        clus
vv                       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               2               135
[1] 2 2
[1] FALSE

Clustering(8) Variable = SHROOM4 MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  SHROOM4 MUTATED     3   0
  SHROOM4 WILD-TYPE 169   6
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                3               175 
  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-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY 
       26.89        31.46        29.03         2.27        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-A6GU TCGA-QR-A6GW TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ 
      137.59        58.88        16.14        19.04         1.05        30.51 
TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H4 TCGA-QR-A6H5 
        9.21        14.17         9.93        14.27        87.48        31.53 
TCGA-QR-A6H6 TCGA-QR-A6ZZ TCGA-QR-A702 TCGA-QR-A703 TCGA-QR-A705 TCGA-QR-A706 
       15.58         1.58         1.28        38.37        10.42         4.11 
TCGA-QR-A707 TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E 
       13.08         1.15        69.67       116.19         0.23         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-A70O TCGA-QR-A70P TCGA-QR-A70R TCGA-QR-A70T TCGA-QR-A70U 
        1.41         3.65       117.14        14.20         8.78        48.43 
TCGA-QR-A70V TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ 
        0.07        41.79         6.02        12.39        17.95        36.23 
TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP 
        6.94         1.81         0.72        25.18         2.30         4.41 
TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA 
        0.79        13.08        77.98         0.92       108.26        50.63 
TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 
        8.09        86.89        19.86         2.93         7.10        33.30 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 
       23.80         1.05         0.85        13.32         1.22        11.70 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G 
       13.05         7.96         6.28        72.79        15.02        41.88 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89        20.09        31.59        30.21 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       35.51        31.04        26.96        40.70        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       27.91        20.58        25.32        12.66        18.94        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QH 
        9.73       114.77       109.25        82.62        67.50        72.43 
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-A6MR TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
       68.61        79.20        81.93       106.75       110.53       121.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        19.76        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       19.92        13.32        25.32        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       19.86        12.03        12.49        16.60        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       10.65        34.82        34.26         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      316.73       127.56        29.16        19.59        32.88         5.98 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        34.03        33.90        24.16        35.84        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       57.11        38.76        42.54        22.32        24.36        40.04 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       45.83        53.69        12.99        24.82         1.61        23.77 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 
       18.28        71.05        78.21        10.16        93.11       103.17 
TCGA-XG-A823 
       20.19 

  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             20.19 
[1] "4.6 - 41.2 (37.2)"  "0.1 - 316.7 (20.2)"
[1] "hr="     "9200000"
D8V2, continuous
D8V3, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED     1   2
  SHROOM4 WILD-TYPE 100  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      1    2
  SHROOM4 WILD-TYPE  100   75
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  FEMALE               1               100
  MALE                 2                75
[1] 2 2
[1] FALSE
                   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   144
D8V4, 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               144
[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"
D8V5, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED     1   1
  SHROOM4 WILD-TYPE   4 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      1    1
  SHROOM4 WILD-TYPE    4  136
                        clus
vv                       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               1               136
[1] 2 2
[1] FALSE

Clustering(9) Variable = FAM83D MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2                0   1
  FAM83D MUTATED     3   0
  FAM83D WILD-TYPE 169   6
  FAM83D MUTATED FAM83D WILD-TYPE 
               3              175 
  FAM83D MUTATED FAM83D WILD-TYPE 
               0                6 
$`FAM83D MUTATED`
TCGA-QR-A70K TCGA-RW-A68B TCGA-WB-A81R 
        9.01         7.96         1.61 

$`FAM83D WILD-TYPE`
TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY 
       26.89        31.46        29.03         2.27        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-A6GU TCGA-QR-A6GW TCGA-QR-A6GX TCGA-QR-A6GY TCGA-QR-A6GZ 
      137.59        58.88        16.14        19.04         1.05        30.51 
TCGA-QR-A6H0 TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H4 TCGA-QR-A6H5 
        9.21        14.17         9.93        14.27        87.48        31.53 
TCGA-QR-A6H6 TCGA-QR-A6ZZ TCGA-QR-A702 TCGA-QR-A703 TCGA-QR-A705 TCGA-QR-A706 
       15.58         1.58         1.28        38.37        10.42         4.11 
TCGA-QR-A707 TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C TCGA-QR-A70D TCGA-QR-A70E 
       13.08         1.15        69.67       116.19         0.23         6.31 
TCGA-QR-A70G TCGA-QR-A70H TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70M TCGA-QR-A70N 
        2.33        26.83        29.92        13.12        33.99         1.41 
TCGA-QR-A70O TCGA-QR-A70P TCGA-QR-A70Q TCGA-QR-A70R TCGA-QR-A70T TCGA-QR-A70U 
        3.65       117.14         4.60        14.20         8.78        48.43 
TCGA-QR-A70V TCGA-QR-A70W TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ 
        0.07        41.79         6.02        12.39        17.95        36.23 
TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP 
        6.94         1.81         0.72        25.18         2.30         4.41 
TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA 
        0.79        13.08        77.98         0.92       108.26        50.63 
TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 
        8.09        86.89        19.86         2.93         7.10        33.30 
TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 
       23.80         1.05         0.85        13.32         1.22        11.70 
TCGA-RW-A68A TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
       13.05         6.28        72.79        15.02        41.88         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89        20.09        31.59        30.21        37.25 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       35.51        31.04        26.96        40.70        37.58        30.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       27.91        20.58        25.32        12.66        18.94        18.08 
TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QH 
        9.73       114.77       109.25        82.62        67.50        72.43 
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-A6MR TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
       68.61        79.20        81.93       106.75       110.53       121.05 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        19.76        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
       19.92        13.32        25.32        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       19.86        12.03        12.49        16.60        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       10.65        34.82        34.26         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      316.73       127.56        29.16        19.59        32.88         5.98 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
       41.23        32.61        34.03        33.90        24.16        35.84 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        57.11        38.76        42.54        22.32        24.36 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81S 
       40.04        45.83        53.69        12.99        24.82        23.77 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 TCGA-WB-A821 TCGA-WB-A822 
       18.28        71.05        78.21        10.16        93.11       103.17 
TCGA-XG-A823 
       20.19 

  FAM83D MUTATED FAM83D WILD-TYPE 
            1.61             0.07 
  FAM83D MUTATED FAM83D WILD-TYPE 
            9.01           316.73 
  FAM83D MUTATED FAM83D WILD-TYPE 
            7.96            22.32 
[1] "1.6 - 9.0 (8.0)"    "0.1 - 316.7 (22.3)"
[1] "hr="     "3300000"
D9V2, continuous
D9V3, binary
                  cls
clus                 0   1
  FAM83D MUTATED     1   2
  FAM83D WILD-TYPE 100  75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM83D MUTATED      1    2
  FAM83D WILD-TYPE  100   75
        clus
vv       FAM83D MUTATED FAM83D WILD-TYPE
  FEMALE              1              100
  MALE                2               75
[1] 2 2
[1] FALSE
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM83D MUTATED                                  0     0
  FAM83D WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM83D MUTATED                           0     2
  FAM83D WILD-TYPE                        20   145
D9V4, multiclass
[1] "Remove cluster labels:" "FAM83D MUTATED"        
clus
  FAM83D MUTATED FAM83D WILD-TYPE 
               2              172 
      TCGA-P7-A5NX       TCGA-P7-A5NY       TCGA-P8-A5KC       TCGA-P8-A5KD 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-P8-A6RX       TCGA-P8-A6RY       TCGA-PR-A5PF       TCGA-PR-A5PG 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-PR-A5PH       TCGA-QR-A6GO       TCGA-QR-A6GR       TCGA-QR-A6GS 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-QR-A6GT       TCGA-QR-A6GU       TCGA-QR-A6GW       TCGA-QR-A6GX 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-QR-A6GY       TCGA-QR-A6GZ       TCGA-QR-A6H0       TCGA-QR-A6H1 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-QR-A6H2       TCGA-QR-A6H3       TCGA-QR-A6H4       TCGA-QR-A6H5 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-QR-A6H6       TCGA-QR-A6ZZ       TCGA-QR-A702       TCGA-QR-A703 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-QR-A705       TCGA-QR-A706       TCGA-QR-A707       TCGA-QR-A708 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-QR-A70A       TCGA-QR-A70C       TCGA-QR-A70D       TCGA-QR-A70E 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-QR-A70G       TCGA-QR-A70H       TCGA-QR-A70I       TCGA-QR-A70J 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-QR-A70M       TCGA-QR-A70N       TCGA-QR-A70O       TCGA-QR-A70P 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-QR-A70Q       TCGA-QR-A70R       TCGA-QR-A70T       TCGA-QR-A70U 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-QR-A70W       TCGA-QR-A70X       TCGA-QR-A7IN       TCGA-QR-A7IP 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-QT-A5XJ       TCGA-QT-A5XK       TCGA-QT-A5XL       TCGA-QT-A5XM 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-QT-A5XN       TCGA-QT-A5XO       TCGA-QT-A5XP       TCGA-QT-A69Q 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-QT-A7U0       TCGA-RM-A68T       TCGA-RM-A68W       TCGA-RT-A6Y9 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-RT-A6YA       TCGA-RT-A6YC       TCGA-RW-A67V       TCGA-RW-A67W 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-RW-A67X       TCGA-RW-A67Y       TCGA-RW-A680       TCGA-RW-A681 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-RW-A684       TCGA-RW-A685       TCGA-RW-A686       TCGA-RW-A688 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-RW-A689       TCGA-RW-A68A       TCGA-RW-A68C       TCGA-RW-A68D 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-RW-A68F       TCGA-RW-A68G       TCGA-RW-A7CZ       TCGA-RW-A7D0 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-RW-A8AZ       TCGA-RX-A8JQ       TCGA-S7-A7WL       TCGA-S7-A7WM 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-S7-A7WN       TCGA-S7-A7WO       TCGA-S7-A7WP       TCGA-S7-A7WQ 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-S7-A7WR       TCGA-S7-A7WT       TCGA-S7-A7WU       TCGA-S7-A7WV 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-S7-A7WW       TCGA-S7-A7WX       TCGA-S7-A7X0       TCGA-S7-A7X1 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-S7-A7X2       TCGA-SA-A6C2       TCGA-SP-A6QC       TCGA-SP-A6QF 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-SP-A6QG       TCGA-SP-A6QH       TCGA-SP-A6QI       TCGA-SP-A6QJ 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-SP-A6QK       TCGA-SQ-A6I4       TCGA-SQ-A6I6       TCGA-SR-A6MP 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-SR-A6MQ       TCGA-SR-A6MR       TCGA-SR-A6MS       TCGA-SR-A6MT 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-SR-A6MU       TCGA-SR-A6MV       TCGA-SR-A6MX       TCGA-SR-A6MY 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-SR-A6MZ       TCGA-SR-A6N0       TCGA-TT-A6YK       TCGA-TT-A6YN 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-TT-A6YO       TCGA-TT-A6YP       TCGA-W2-A7H5       TCGA-W2-A7H7 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-W2-A7HA       TCGA-W2-A7HB       TCGA-W2-A7HC       TCGA-W2-A7HD 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-W2-A7HE       TCGA-W2-A7HF       TCGA-W2-A7HH       TCGA-W2-A7UY 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-WB-A80K       TCGA-WB-A80L       TCGA-WB-A80M       TCGA-WB-A80N 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-WB-A80O       TCGA-WB-A80P       TCGA-WB-A80Q       TCGA-WB-A80V 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-WB-A80Y       TCGA-WB-A814       TCGA-WB-A815       TCGA-WB-A816 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-WB-A817       TCGA-WB-A818       TCGA-WB-A819       TCGA-WB-A81A 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-WB-A81D       TCGA-WB-A81E       TCGA-WB-A81F       TCGA-WB-A81G 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-WB-A81H       TCGA-WB-A81I       TCGA-WB-A81J       TCGA-WB-A81K 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-WB-A81M       TCGA-WB-A81N       TCGA-WB-A81P       TCGA-WB-A81Q 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-WB-A81S       TCGA-WB-A81T       TCGA-WB-A81V       TCGA-WB-A81W 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
      TCGA-WB-A820       TCGA-WB-A821       TCGA-WB-A822       TCGA-XG-A823 
"FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" "FAM83D WILD-TYPE" 
D9V5, binary
                  cls
clus                 0   1
  FAM83D MUTATED     0   2
  FAM83D WILD-TYPE   5 135
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM83D MUTATED      0    2
  FAM83D WILD-TYPE    5  135
                        clus
vv                       FAM83D MUTATED FAM83D WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2              135
[1] 2 2
[1] FALSE
