[1] "ofn"        "-oTTHYM-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/THYM-TP/22507339/THYM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THYM-TP/22571831/transformed.cor.cli.txt"

nPatients in clinical file=124, in cluster file=120, common to both=120
[1] "Reduce the number of clustering variables from 12 to 8."
[1]   8 120
[1] "GTF2I MUTATION ANALYSIS"
[1] 3
  GTF2I MUTATED GTF2I WILD-TYPE 
             49              71 
  GTF2I MUTATED GTF2I WILD-TYPE 
             49              71 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            10            110 
  HRAS MUTATED HRAS WILD-TYPE 
            10            110 
[1] "CAPNS1 MUTATION ANALYSIS"
[1] 3
  CAPNS1 MUTATED CAPNS1 WILD-TYPE 
               3              117 
  CAPNS1 MUTATED CAPNS1 WILD-TYPE 
               3              117 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             4            116 
  TP53 MUTATED TP53 WILD-TYPE 
             4            116 
[1] "ATRN MUTATION ANALYSIS"
[1] 3
  ATRN MUTATED ATRN WILD-TYPE 
             3            117 
  ATRN MUTATED ATRN WILD-TYPE 
             3            117 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             3            117 
  NRAS MUTATED NRAS WILD-TYPE 
             3            117 
[1] "PLEKHG4B MUTATION ANALYSIS"
[1] 3
  PLEKHG4B MUTATED PLEKHG4B WILD-TYPE 
                 3                117 
  PLEKHG4B MUTATED PLEKHG4B WILD-TYPE 
                 3                117 
[1] "UNC93B1 MUTATION ANALYSIS"
[1] 3
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                5               115 
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                5               115 
[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] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RACE"                                
[15] "ETHNICITY"                           

Input Data has 15 rows and 120 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=9,	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=107,	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:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'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 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'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 120 columns, 1 survival variables, and 7 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" "GENDER"           
[4] "RADIATION_THERAPY" "HISTOLOGICAL_TYPE" "RACE"             
[7] "ETHNICITY"        
YEARS_TO_BIRTH, nv=48, 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
HISTOLOGICAL_TYPE, nv=6, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = GTF2I MUTATION ANALYSIS
D1V1, survival
                 sevent
clus2              0  1
  GTF2I MUTATED   46  2
  GTF2I WILD-TYPE 64  7
  GTF2I MUTATED GTF2I WILD-TYPE 
             48              71 
  GTF2I MUTATED GTF2I WILD-TYPE 
              2               7 
$`GTF2I MUTATED`
TCGA-3G-AB19 TCGA-5U-AB0F TCGA-XM-A8RG TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 
       95.67        15.09        12.69        35.90        25.48        26.83 
TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0Q TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       71.11        45.63        59.15        20.61        20.71        14.27 
TCGA-4X-A9FA TCGA-5K-AAAP TCGA-5V-A9RR TCGA-X7-A8D8 TCGA-X7-A8DC TCGA-X7-A8DE 
       12.89        34.65        27.19         1.91        59.11        32.25 
TCGA-X7-A8DF TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M5 
       29.62        23.18         9.50        14.50        42.15        54.08 
TCGA-XM-A8RF TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       26.20        32.25        37.81       112.11        90.05        45.24 
TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-AAY0 TCGA-YT-A95D TCGA-YT-A95E TCGA-ZB-A962 
      149.98         4.08        49.38        24.66        35.18        54.15 
TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96D TCGA-ZB-A96E 
       48.72        42.31        34.39        77.39        64.44        59.80 
TCGA-ZB-A96H TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96Q TCGA-ZC-AAAF TCGA-ZL-A9V6 
       49.45        50.27         0.46        22.19        38.30        68.91 

$`GTF2I WILD-TYPE`
TCGA-4X-A9FB TCGA-XM-A8RD TCGA-XM-AAZ1 TCGA-3G-AB0O TCGA-3G-AB0T TCGA-3G-AB14 
       23.57        50.83        13.05        68.58        81.80        25.48 
TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ 
       15.35        21.14        18.77        34.52        96.53        93.67 
TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS 
       62.73        41.19        31.89        51.68        25.64        25.45 
TCGA-4V-A9QT TCGA-4X-A9F9 TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0D 
       26.73        21.99        68.12        49.41        27.45        23.47 
TCGA-5U-AB0E TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8DB TCGA-X7-A8DD TCGA-X7-A8DG 
       22.59       138.90        10.68        65.49        36.62        22.85 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M6 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
        1.64       125.19       150.41        83.28        40.11        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RH TCGA-XM-A8RI 
       48.92        37.61        97.41        13.87        11.93        12.72 
TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 
      107.80        77.03       114.67       120.43        82.65        52.90 
TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY 
       70.65        58.82        21.14       123.68        89.46        62.17 
TCGA-XU-AAXZ TCGA-XU-AAY1 TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A966 
       50.53       107.44        49.78        23.38         5.92        12.46 
TCGA-ZB-A96B TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96I TCGA-ZB-A96O TCGA-ZB-A96R 
       72.69        57.90        52.80        54.35        34.52        59.31 
TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAH TCGA-ZT-A8OM 
       30.64        28.04        26.93        16.34        45.96 

  GTF2I MUTATED GTF2I WILD-TYPE 
           0.46            1.64 
  GTF2I MUTATED GTF2I WILD-TYPE 
         149.98          150.41 
  GTF2I MUTATED GTF2I WILD-TYPE 
          35.54           48.92 
[1] "0.5 - 150.0 (35.5)" "1.6 - 150.4 (48.9)"
[1] "hr=" "1.7"
D1V2, continuous
D1V3, binary
                 cls
clus               0  1
  GTF2I MUTATED    9 40
  GTF2I WILD-TYPE 16 55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTF2I MUTATED      9   40
  GTF2I WILD-TYPE   16   55
                      clus
vv                     GTF2I MUTATED GTF2I WILD-TYPE
  ANTERIOR MEDIASTINUM             9              16
  THYMUS                          40              55
[1] 2 2
[1] FALSE
D1V4, binary
                 cls
clus               0  1
  GTF2I MUTATED   23 26
  GTF2I WILD-TYPE 36 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTF2I MUTATED     23   26
  GTF2I WILD-TYPE   36   35
        clus
vv       GTF2I MUTATED GTF2I WILD-TYPE
  FEMALE            23              36
  MALE              26              35
[1] 2 2
[1] FALSE
D1V5, binary
                 cls
clus               0  1
  GTF2I MUTATED   39 10
  GTF2I WILD-TYPE 39 32
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTF2I MUTATED     39   10
  GTF2I WILD-TYPE   39   32
     clus
vv    GTF2I MUTATED GTF2I WILD-TYPE
  NO             39              39
  YES            10              32
[1] 2 2
[1] FALSE
                 vv
clus              THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  GTF2I MUTATED                14               27                0
  GTF2I WILD-TYPE               3               11               13
                 vv
clus              THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  GTF2I MUTATED                  5                2               1
  GTF2I WILD-TYPE               24               10              10
D1V6, multiclass
                  clus
vv                 GTF2I MUTATED GTF2I WILD-TYPE
  THYMOMA; TYPE A             14               3
  THYMOMA; TYPE AB            27              11
  THYMOMA; TYPE B1             0              13
  THYMOMA; TYPE B2             5              24
  THYMOMA; TYPE B3             2              10
  THYMOMA; TYPE C              1              10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GTF2I MUTATED       6                         1    41
  GTF2I WILD-TYPE     7                         5    58
D1V7, multiclass
                           clus
vv                          GTF2I MUTATED GTF2I WILD-TYPE
  ASIAN                                 6               7
  BLACK OR AFRICAN AMERICAN             1               5
  WHITE                                41              58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
                 cls
clus               0  1
  GTF2I MUTATED    3 40
  GTF2I WILD-TYPE  6 57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTF2I MUTATED      3   40
  GTF2I WILD-TYPE    6   57
                        clus
vv                       GTF2I MUTATED GTF2I WILD-TYPE
  HISPANIC OR LATINO                 3               6
  NOT HISPANIC OR LATINO            40              57
[1] 2 2
[1] FALSE

Clustering(2) Variable = HRAS MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  HRAS MUTATED     9   1
  HRAS WILD-TYPE 101   8
  HRAS MUTATED HRAS WILD-TYPE 
            10            109 
  HRAS MUTATED HRAS WILD-TYPE 
             1              8 
$`HRAS MUTATED`
TCGA-3G-AB19 TCGA-XM-A8RG TCGA-XU-A92Q TCGA-ZB-A965 TCGA-XM-AAZ3 TCGA-XU-A92T 
       95.67        12.69        35.90        26.83        37.81        45.24 
TCGA-ZB-A962 TCGA-ZB-A964 TCGA-ZB-A96E TCGA-ZL-A9V6 
       54.15        42.31        59.80        68.91 

$`HRAS WILD-TYPE`
TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-AAZ1 TCGA-YT-A95F TCGA-ZB-A96C 
       23.57        15.09        50.83        13.05        25.48        71.11 
TCGA-ZB-A96K TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF 
       45.63        68.58        59.15        81.80        25.48        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       21.14        18.77        34.52        96.53        93.67        62.73 
TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT 
       41.19        31.89        51.68        25.64        25.45        26.73 
TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC 
       20.61        20.71        14.27        21.99        12.89        68.12 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5V-A9RR 
       49.41        27.45        34.65        23.47        22.59        27.19 
TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD 
      138.90        10.68         1.91        65.49        59.11        36.62 
TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 
       32.25        29.62        22.85        23.18         9.50        14.50 
TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M8 
       42.15         1.64       125.19        54.08       150.41        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RE 
       40.11        52.54        48.92        37.61        97.41        13.87 
TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-AAZ2 TCGA-XU-A92O TCGA-XU-A92R 
       26.20        11.93        12.72        32.25       112.11        90.05 
TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z 
      149.98         4.08       107.80        77.03       114.67       120.43 
TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXW 
       82.65        52.90        70.65        58.82        21.14       123.68 
TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D 
       89.46        62.17        50.53        49.38       107.44        24.66 
TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A963 TCGA-ZB-A966 
       35.18        49.78        23.38         5.92        48.72        12.46 
TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96F TCGA-ZB-A96G 
       34.39        77.39        72.69        64.44        57.90        52.80 
TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96Q 
       49.45        54.35        50.27         0.46        34.52        22.19 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
       59.31        30.64        28.04        26.93        38.30        16.34 
TCGA-ZT-A8OM 
       45.96 

  HRAS MUTATED HRAS WILD-TYPE 
         12.69           0.46 
  HRAS MUTATED HRAS WILD-TYPE 
         95.67         150.41 
  HRAS MUTATED HRAS WILD-TYPE 
        43.775         38.300 
[1] "12.7 - 95.7 (43.8)" "0.5 - 150.4 (38.3)"
[1] "hr=" "1.5"
D2V2, continuous
D2V3, binary
                cls
clus              0  1
  HRAS MUTATED    1  9
  HRAS WILD-TYPE 24 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      1    9
  HRAS WILD-TYPE   24   86
                      clus
vv                     HRAS MUTATED HRAS WILD-TYPE
  ANTERIOR MEDIASTINUM            1             24
  THYMUS                          9             86
[1] 2 2
[1] FALSE
D2V4, binary
                cls
clus              0  1
  HRAS MUTATED    3  7
  HRAS WILD-TYPE 56 54
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      3    7
  HRAS WILD-TYPE   56   54
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  FEMALE            3             56
  MALE              7             54
[1] 2 2
[1] FALSE
D2V5, binary
                cls
clus              0  1
  HRAS MUTATED    7  3
  HRAS WILD-TYPE 71 39
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      7    3
  HRAS WILD-TYPE   71   39
     clus
vv    HRAS MUTATED HRAS WILD-TYPE
  NO             7             71
  YES            3             39
[1] 2 2
[1] FALSE
                vv
clus             THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  HRAS MUTATED                 7                3                0
  HRAS WILD-TYPE              10               35               13
                vv
clus             THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  HRAS MUTATED                  0                0               0
  HRAS WILD-TYPE               29               12              11
D2V6, multiclass
                  clus
vv                 HRAS MUTATED HRAS WILD-TYPE
  THYMOMA; TYPE A             7             10
  THYMOMA; TYPE AB            3             35
  THYMOMA; TYPE B1            0             13
  THYMOMA; TYPE B2            0             29
  THYMOMA; TYPE B3            0             12
  THYMOMA; TYPE C             0             11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HRAS MUTATED       1                         0     9
  HRAS WILD-TYPE    12                         6    90
D2V7, multiclass
                           clus
vv                          HRAS MUTATED HRAS WILD-TYPE
  ASIAN                                1             12
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                9             90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                cls
clus              0  1
  HRAS MUTATED    0  8
  HRAS WILD-TYPE  9 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0    8
  HRAS WILD-TYPE    9   89
                        clus
vv                       HRAS MUTATED HRAS WILD-TYPE
  HISPANIC OR LATINO                0              9
  NOT HISPANIC OR LATINO            8             89
[1] 2 2
[1] FALSE

Clustering(3) Variable = CAPNS1 MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2                0   1
  CAPNS1 MUTATED     3   0
  CAPNS1 WILD-TYPE 107   9
  CAPNS1 MUTATED CAPNS1 WILD-TYPE 
               3              116 
  CAPNS1 MUTATED CAPNS1 WILD-TYPE 
               0                9 
$`CAPNS1 MUTATED`
TCGA-4V-A9QL TCGA-4V-A9QT TCGA-4V-A9QX 
       62.73        26.73        14.27 

$`CAPNS1 WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-AAZ1 
       95.67        23.57        15.09        50.83        12.69        13.05 
TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O 
       35.90        25.48        26.83        71.11        45.63        68.58 
TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX 
       59.15        81.80        25.48        15.35        21.14        18.77 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ 
       34.52        96.53        93.67        41.19        31.89        51.68 
TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4X-A9F9 TCGA-4X-A9FA 
       25.64        25.45        20.61        20.71        21.99        12.89 
TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E 
       68.12        49.41        27.45        34.65        23.47        22.59 
TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC 
       27.19       138.90        10.68         1.91        65.49        59.11 
TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ 
       36.62        32.25        29.62        22.85        23.18         9.50 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 
       14.50        42.15         1.64       125.19        54.08       150.41 
TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC 
       83.28        40.11        52.54        48.92        37.61        97.41 
TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       13.87        26.20        11.93        12.72        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W 
      112.11        90.05        45.24       149.98         4.08       107.80 
TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 
       77.03       114.67       120.43        82.65        52.90        70.65 
TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ 
       58.82        21.14       123.68        89.46        62.17        50.53 
TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H 
       49.38       107.44        24.66        35.18        49.78        23.38 
TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A969 
        5.92        54.15        48.72        42.31        12.46        34.39 
TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G 
       77.39        72.69        64.44        59.80        57.90        52.80 
TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96Q 
       49.45        54.35        50.27         0.46        34.52        22.19 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
       59.31        30.64        28.04        26.93        38.30        16.34 
TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       68.91        45.96 

  CAPNS1 MUTATED CAPNS1 WILD-TYPE 
           14.27             0.46 
  CAPNS1 MUTATED CAPNS1 WILD-TYPE 
           62.73           150.41 
  CAPNS1 MUTATED CAPNS1 WILD-TYPE 
           26.73            40.65 
[1] "14.3 - 62.7 (26.7)" "0.5 - 150.4 (40.6)"
[1] "hr="     "9200000"
D3V2, continuous
D3V3, binary
                  cls
clus                0  1
  CAPNS1 MUTATED    0  3
  CAPNS1 WILD-TYPE 25 92
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAPNS1 MUTATED      0    3
  CAPNS1 WILD-TYPE   25   92
                      clus
vv                     CAPNS1 MUTATED CAPNS1 WILD-TYPE
  ANTERIOR MEDIASTINUM              0               25
  THYMUS                            3               92
[1] 2 2
[1] FALSE
D3V4, binary
                  cls
clus                0  1
  CAPNS1 MUTATED    3  0
  CAPNS1 WILD-TYPE 56 61
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAPNS1 MUTATED      3    0
  CAPNS1 WILD-TYPE   56   61
        clus
vv       CAPNS1 MUTATED CAPNS1 WILD-TYPE
  FEMALE              3               56
  MALE                0               61
[1] 2 2
[1] FALSE
D3V5, binary
                  cls
clus                0  1
  CAPNS1 MUTATED    2  1
  CAPNS1 WILD-TYPE 76 41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAPNS1 MUTATED      2    1
  CAPNS1 WILD-TYPE   76   41
     clus
vv    CAPNS1 MUTATED CAPNS1 WILD-TYPE
  NO               2               76
  YES              1               41
[1] 2 2
[1] FALSE
                  vv
clus               THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  CAPNS1 MUTATED                 0                2                1
  CAPNS1 WILD-TYPE              17               36               12
                  vv
clus               THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  CAPNS1 MUTATED                  0                0               0
  CAPNS1 WILD-TYPE               29               12              11
D3V6, multiclass
                  clus
vv                 CAPNS1 MUTATED CAPNS1 WILD-TYPE
  THYMOMA; TYPE A               0               17
  THYMOMA; TYPE AB              2               36
  THYMOMA; TYPE B1              1               12
  THYMOMA; TYPE B2              0               29
  THYMOMA; TYPE B3              0               12
  THYMOMA; TYPE C               0               11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CAPNS1 MUTATED       0                         0     3
  CAPNS1 WILD-TYPE    13                         6    96
D3V7, multiclass
                           clus
vv                          CAPNS1 MUTATED CAPNS1 WILD-TYPE
  ASIAN                                  0               13
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  3               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                  cls
clus                0  1
  CAPNS1 MUTATED    0  3
  CAPNS1 WILD-TYPE  9 94
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAPNS1 MUTATED      0    3
  CAPNS1 WILD-TYPE    9   94
                        clus
vv                       CAPNS1 MUTATED CAPNS1 WILD-TYPE
  HISPANIC OR LATINO                  0                9
  NOT HISPANIC OR LATINO              3               94
[1] 2 2
[1] FALSE

Clustering(4) Variable = TP53 MUTATION ANALYSIS
D4V1, survival
                sevent
clus2              0   1
  TP53 MUTATED     2   2
  TP53 WILD-TYPE 108   7
  TP53 MUTATED TP53 WILD-TYPE 
             4            115 
  TP53 MUTATED TP53 WILD-TYPE 
             2              7 
$`TP53 MUTATED`
TCGA-3G-AB14 TCGA-3S-A8YW TCGA-4V-A9QJ TCGA-ZB-A966 
       25.48        21.14        93.67        12.46 

$`TP53 WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-AAZ1 
       95.67        23.57        15.09        50.83        12.69        13.05 
TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O 
       35.90        25.48        26.83        71.11        45.63        68.58 
TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI 
       59.15        81.80        15.35        18.77        34.52        96.53 
TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS 
       62.73        41.19        31.89        51.68        25.64        25.45 
TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA 
       26.73        20.61        20.71        14.27        21.99        12.89 
TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E 
       68.12        49.41        27.45        34.65        23.47        22.59 
TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC 
       27.19       138.90        10.68         1.91        65.49        59.11 
TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ 
       36.62        32.25        29.62        22.85        23.18         9.50 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 
       14.50        42.15         1.64       125.19        54.08       150.41 
TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC 
       83.28        40.11        52.54        48.92        37.61        97.41 
TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       13.87        26.20        11.93        12.72        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W 
      112.11        90.05        45.24       149.98         4.08       107.80 
TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 
       77.03       114.67       120.43        82.65        52.90        70.65 
TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ 
       58.82        21.14       123.68        89.46        62.17        50.53 
TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H 
       49.38       107.44        24.66        35.18        49.78        23.38 
TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A969 TCGA-ZB-A96A 
        5.92        54.15        48.72        42.31        34.39        77.39 
TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H 
       72.69        64.44        59.80        57.90        52.80        49.45 
TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96Q TCGA-ZB-A96R 
       54.35        50.27         0.46        34.52        22.19        59.31 
TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       30.64        28.04        26.93        38.30        16.34        68.91 
TCGA-ZT-A8OM 
       45.96 

  TP53 MUTATED TP53 WILD-TYPE 
         12.46           0.46 
  TP53 MUTATED TP53 WILD-TYPE 
         93.67         150.41 
  TP53 MUTATED TP53 WILD-TYPE 
         23.31          41.19 
[1] "12.5 - 93.7 (23.3)" "0.5 - 150.4 (41.2)"
[1] "hr=" "13" 
D4V2, continuous
D4V3, binary
                cls
clus              0  1
  TP53 MUTATED    0  4
  TP53 WILD-TYPE 25 91
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      0    4
  TP53 WILD-TYPE   25   91
                      clus
vv                     TP53 MUTATED TP53 WILD-TYPE
  ANTERIOR MEDIASTINUM            0             25
  THYMUS                          4             91
[1] 2 2
[1] FALSE
D4V4, binary
                cls
clus              0  1
  TP53 MUTATED    1  3
  TP53 WILD-TYPE 58 58
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1    3
  TP53 WILD-TYPE   58   58
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            1             58
  MALE              3             58
[1] 2 2
[1] FALSE
D4V5, binary
                cls
clus              0  1
  TP53 MUTATED    1  3
  TP53 WILD-TYPE 77 39
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1    3
  TP53 WILD-TYPE   77   39
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO             1             77
  YES            3             39
[1] 2 2
[1] FALSE
                vv
clus             THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  TP53 MUTATED                 0                0                0
  TP53 WILD-TYPE              17               38               13
                vv
clus             THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  TP53 MUTATED                  1                1               2
  TP53 WILD-TYPE               28               11               9
D4V6, multiclass
                  clus
vv                 TP53 MUTATED TP53 WILD-TYPE
  THYMOMA; TYPE A             0             17
  THYMOMA; TYPE AB            0             38
  THYMOMA; TYPE B1            0             13
  THYMOMA; TYPE B2            1             28
  THYMOMA; TYPE B3            1             11
  THYMOMA; TYPE C             2              9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       0                         0     4
  TP53 WILD-TYPE    13                         6    95
D4V7, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                0             13
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                4             95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                cls
clus              0  1
  TP53 MUTATED    1  3
  TP53 WILD-TYPE  8 94
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1    3
  TP53 WILD-TYPE    8   94
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                1              8
  NOT HISPANIC OR LATINO            3             94
[1] 2 2
[1] FALSE

Clustering(5) Variable = ATRN MUTATION ANALYSIS
D5V1, survival
                sevent
clus2              0   1
  ATRN MUTATED     3   0
  ATRN WILD-TYPE 107   9
  ATRN MUTATED ATRN WILD-TYPE 
             3            116 
  ATRN MUTATED ATRN WILD-TYPE 
             0              9 
$`ATRN MUTATED`
TCGA-X7-A8DF TCGA-XU-A92O TCGA-ZB-A969 
       29.62       112.11        34.39 

$`ATRN WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-AAZ1 
       95.67        23.57        15.09        50.83        12.69        13.05 
TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O 
       35.90        25.48        26.83        71.11        45.63        68.58 
TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX 
       59.15        81.80        25.48        15.35        21.14        18.77 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN 
       34.52        96.53        93.67        62.73        41.19        31.89 
TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW 
       51.68        25.64        25.45        26.73        20.61        20.71 
TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ 
       14.27        21.99        12.89        68.12        49.41        27.45 
TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 
       34.65        23.47        22.59        27.19       138.90        10.68 
TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DG 
        1.91        65.49        59.11        36.62        32.25        22.85 
TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 
       23.18         9.50        14.50        42.15         1.64       125.19 
TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
       54.08       150.41        83.28        40.11        52.54        48.92 
TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI 
       37.61        97.41        13.87        26.20        11.93        12.72 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
       32.25        37.81        90.05        45.24       149.98         4.08 
TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 
      107.80        77.03       114.67       120.43        82.65        52.90 
TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY 
       70.65        58.82        21.14       123.68        89.46        62.17 
TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95G 
       50.53        49.38       107.44        24.66        35.18        49.78 
TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 
       23.38         5.92        54.15        48.72        42.31        12.46 
TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G 
       77.39        72.69        64.44        59.80        57.90        52.80 
TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96Q 
       49.45        54.35        50.27         0.46        34.52        22.19 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
       59.31        30.64        28.04        26.93        38.30        16.34 
TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       68.91        45.96 

  ATRN MUTATED ATRN WILD-TYPE 
         29.62           0.46 
  ATRN MUTATED ATRN WILD-TYPE 
        112.11         150.41 
  ATRN MUTATED ATRN WILD-TYPE 
         34.39          40.65 
[1] "29.6 - 112.1 (34.4)" "0.5 - 150.4 (40.6)" 
[1] "hr="     "2.6e+07"
D5V2, continuous
D5V3, binary
                cls
clus              0  1
  ATRN MUTATED    1  2
  ATRN WILD-TYPE 24 93
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRN MUTATED      1    2
  ATRN WILD-TYPE   24   93
                      clus
vv                     ATRN MUTATED ATRN WILD-TYPE
  ANTERIOR MEDIASTINUM            1             24
  THYMUS                          2             93
[1] 2 2
[1] FALSE
D5V4, binary
                cls
clus              0  1
  ATRN MUTATED    1  2
  ATRN WILD-TYPE 58 59
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRN MUTATED      1    2
  ATRN WILD-TYPE   58   59
        clus
vv       ATRN MUTATED ATRN WILD-TYPE
  FEMALE            1             58
  MALE              2             59
[1] 2 2
[1] FALSE
D5V5, binary
                cls
clus              0  1
  ATRN MUTATED    3  0
  ATRN WILD-TYPE 75 42
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRN MUTATED      3    0
  ATRN WILD-TYPE   75   42
     clus
vv    ATRN MUTATED ATRN WILD-TYPE
  NO             3             75
  YES            0             42
[1] 2 2
[1] FALSE
                vv
clus             THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  ATRN MUTATED                 1                1                0
  ATRN WILD-TYPE              16               37               13
                vv
clus             THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  ATRN MUTATED                  0                0               1
  ATRN WILD-TYPE               29               12              10
D5V6, multiclass
                  clus
vv                 ATRN MUTATED ATRN WILD-TYPE
  THYMOMA; TYPE A             1             16
  THYMOMA; TYPE AB            1             37
  THYMOMA; TYPE B1            0             13
  THYMOMA; TYPE B2            0             29
  THYMOMA; TYPE B3            0             12
  THYMOMA; TYPE C             1             10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATRN MUTATED       1                         0     2
  ATRN WILD-TYPE    12                         6    97
D5V7, multiclass
                           clus
vv                          ATRN MUTATED ATRN WILD-TYPE
  ASIAN                                1             12
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                2             97
[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, binary
                cls
clus              0  1
  ATRN MUTATED    0  3
  ATRN WILD-TYPE  9 94
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRN MUTATED      0    3
  ATRN WILD-TYPE    9   94
                        clus
vv                       ATRN MUTATED ATRN WILD-TYPE
  HISPANIC OR LATINO                0              9
  NOT HISPANIC OR LATINO            3             94
[1] 2 2
[1] FALSE

Clustering(6) Variable = NRAS MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  NRAS MUTATED     3   0
  NRAS WILD-TYPE 107   9
  NRAS MUTATED NRAS WILD-TYPE 
             3            116 
  NRAS MUTATED NRAS WILD-TYPE 
             0              9 
$`NRAS MUTATED`
TCGA-XM-AAZ1 TCGA-XU-A92O TCGA-XU-A92Z 
       13.05       112.11       120.43 

$`NRAS WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XU-A92Q 
       95.67        23.57        15.09        50.83        12.69        35.90 
TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O TCGA-3G-AB0Q 
       25.48        26.83        71.11        45.63        68.58        59.15 
TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L 
       81.80        25.48        15.35        21.14        18.77        34.52 
TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ 
       96.53        93.67        62.73        41.19        31.89        51.68 
TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       25.64        25.45        26.73        20.61        20.71        14.27 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP 
       21.99        12.89        68.12        49.41        27.45        34.65 
TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 
       23.47        22.59        27.19       138.90        10.68         1.91 
TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG 
       65.49        59.11        36.62        32.25        29.62        22.85 
TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 
       23.18         9.50        14.50        42.15         1.64       125.19 
TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
       54.08       150.41        83.28        40.11        52.54        48.92 
TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI 
       37.61        97.41        13.87        26.20        11.93        12.72 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
       32.25        37.81        90.05        45.24       149.98         4.08 
TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 
      107.80        77.03       114.67        82.65        52.90        70.65 
TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ 
       58.82        21.14       123.68        89.46        62.17        50.53 
TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H 
       49.38       107.44        24.66        35.18        49.78        23.38 
TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A969 
        5.92        54.15        48.72        42.31        12.46        34.39 
TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G 
       77.39        72.69        64.44        59.80        57.90        52.80 
TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96Q 
       49.45        54.35        50.27         0.46        34.52        22.19 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
       59.31        30.64        28.04        26.93        38.30        16.34 
TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       68.91        45.96 

  NRAS MUTATED NRAS WILD-TYPE 
         13.05           0.46 
  NRAS MUTATED NRAS WILD-TYPE 
        120.43         150.41 
  NRAS MUTATED NRAS WILD-TYPE 
       112.110         39.205 
[1] "13.1 - 120.4 (112.1)" "0.5 - 150.4 (39.2)"  
[1] "hr="     "7.9e+07"
D6V2, continuous
D6V3, binary
                cls
clus              0  1
  NRAS MUTATED    1  2
  NRAS WILD-TYPE 24 93
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      1    2
  NRAS WILD-TYPE   24   93
                      clus
vv                     NRAS MUTATED NRAS WILD-TYPE
  ANTERIOR MEDIASTINUM            1             24
  THYMUS                          2             93
[1] 2 2
[1] FALSE
D6V4, binary
                cls
clus              0  1
  NRAS MUTATED    0  3
  NRAS WILD-TYPE 59 58
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0    3
  NRAS WILD-TYPE   59   58
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            0             59
  MALE              3             58
[1] 2 2
[1] FALSE
D6V5, binary
                cls
clus              0  1
  NRAS MUTATED    1  2
  NRAS WILD-TYPE 77 40
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      1    2
  NRAS WILD-TYPE   77   40
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             1             77
  YES            2             40
[1] 2 2
[1] FALSE
                vv
clus             THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  NRAS MUTATED                 1                0                0
  NRAS WILD-TYPE              16               38               13
                vv
clus             THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  NRAS MUTATED                  1                0               1
  NRAS WILD-TYPE               28               12              10
D6V6, multiclass
                  clus
vv                 NRAS MUTATED NRAS WILD-TYPE
  THYMOMA; TYPE A             1             16
  THYMOMA; TYPE AB            0             38
  THYMOMA; TYPE B1            0             13
  THYMOMA; TYPE B2            1             28
  THYMOMA; TYPE B3            0             12
  THYMOMA; TYPE C             1             10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED       2                         0     1
  NRAS WILD-TYPE    11                         6    98
D6V7, multiclass
                           clus
vv                          NRAS MUTATED NRAS WILD-TYPE
  ASIAN                                2             11
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                1             98
[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, binary
                cls
clus              0  1
  NRAS MUTATED    0  3
  NRAS WILD-TYPE  9 94
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0    3
  NRAS WILD-TYPE    9   94
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                0              9
  NOT HISPANIC OR LATINO            3             94
[1] 2 2
[1] FALSE

Clustering(7) Variable = PLEKHG4B MUTATION ANALYSIS
D7V1, survival
                    sevent
clus2                  0   1
  PLEKHG4B MUTATED     2   1
  PLEKHG4B WILD-TYPE 108   8
  PLEKHG4B MUTATED PLEKHG4B WILD-TYPE 
                 3                116 
  PLEKHG4B MUTATED PLEKHG4B WILD-TYPE 
                 1                  8 
$`PLEKHG4B MUTATED`
TCGA-XM-A8RI TCGA-ZB-A966 TCGA-ZB-A96E 
       12.72        12.46        59.80 

$`PLEKHG4B WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-AAZ1 
       95.67        23.57        15.09        50.83        12.69        13.05 
TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O 
       35.90        25.48        26.83        71.11        45.63        68.58 
TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX 
       59.15        81.80        25.48        15.35        21.14        18.77 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN 
       34.52        96.53        93.67        62.73        41.19        31.89 
TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW 
       51.68        25.64        25.45        26.73        20.61        20.71 
TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ 
       14.27        21.99        12.89        68.12        49.41        27.45 
TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 
       34.65        23.47        22.59        27.19       138.90        10.68 
TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF 
        1.91        65.49        59.11        36.62        32.25        29.62 
TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 
       22.85        23.18         9.50        14.50        42.15         1.64 
TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
      125.19        54.08       150.41        83.28        40.11        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH 
       48.92        37.61        97.41        13.87        26.20        11.93 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U 
       32.25        37.81       112.11        90.05        45.24       149.98 
TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A930 
        4.08       107.80        77.03       114.67       120.43        82.65 
TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXW TCGA-XU-AAXX 
       52.90        70.65        58.82        21.14       123.68        89.46 
TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E 
       62.17        50.53        49.38       107.44        24.66        35.18 
TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       49.78        23.38         5.92        54.15        48.72        42.31 
TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96F TCGA-ZB-A96G 
       34.39        77.39        72.69        64.44        57.90        52.80 
TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96Q 
       49.45        54.35        50.27         0.46        34.52        22.19 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
       59.31        30.64        28.04        26.93        38.30        16.34 
TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       68.91        45.96 

  PLEKHG4B MUTATED PLEKHG4B WILD-TYPE 
             12.46               0.46 
  PLEKHG4B MUTATED PLEKHG4B WILD-TYPE 
             59.80             150.41 
  PLEKHG4B MUTATED PLEKHG4B WILD-TYPE 
             12.72              40.65 
[1] "12.5 - 59.8 (12.7)" "0.5 - 150.4 (40.6)"
[1] "hr=" "9.3"
D7V2, continuous
D7V3, binary
                    cls
clus                  0  1
  PLEKHG4B MUTATED    0  3
  PLEKHG4B WILD-TYPE 25 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PLEKHG4B MUTATED      0    3
  PLEKHG4B WILD-TYPE   25   92
                      clus
vv                     PLEKHG4B MUTATED PLEKHG4B WILD-TYPE
  ANTERIOR MEDIASTINUM                0                 25
  THYMUS                              3                 92
[1] 2 2
[1] FALSE
D7V4, binary
                    cls
clus                  0  1
  PLEKHG4B MUTATED    1  2
  PLEKHG4B WILD-TYPE 58 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PLEKHG4B MUTATED      1    2
  PLEKHG4B WILD-TYPE   58   59
        clus
vv       PLEKHG4B MUTATED PLEKHG4B WILD-TYPE
  FEMALE                1                 58
  MALE                  2                 59
[1] 2 2
[1] FALSE
D7V5, binary
                    cls
clus                  0  1
  PLEKHG4B MUTATED    2  1
  PLEKHG4B WILD-TYPE 76 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PLEKHG4B MUTATED      2    1
  PLEKHG4B WILD-TYPE   76   41
     clus
vv    PLEKHG4B MUTATED PLEKHG4B WILD-TYPE
  NO                 2                 76
  YES                1                 41
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  PLEKHG4B MUTATED                 1                0                0
  PLEKHG4B WILD-TYPE              16               38               13
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  PLEKHG4B MUTATED                  1                0               1
  PLEKHG4B WILD-TYPE               28               12              10
D7V6, multiclass
                  clus
vv                 PLEKHG4B MUTATED PLEKHG4B WILD-TYPE
  THYMOMA; TYPE A                 1                 16
  THYMOMA; TYPE AB                0                 38
  THYMOMA; TYPE B1                0                 13
  THYMOMA; TYPE B2                1                 28
  THYMOMA; TYPE B3                0                 12
  THYMOMA; TYPE C                 1                 10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLEKHG4B MUTATED       0                         0     2
  PLEKHG4B WILD-TYPE    13                         6    97
D7V7, multiclass
[1] "Remove cluster labels:" "PLEKHG4B MUTATED"      
clus
  PLEKHG4B MUTATED PLEKHG4B WILD-TYPE 
                 2                116 
        TCGA-3G-AB19         TCGA-4X-A9FB         TCGA-5U-AB0F 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XM-A8RD         TCGA-XM-A8RG         TCGA-XM-AAZ1 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XU-A92Q         TCGA-YT-A95F         TCGA-ZB-A965 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZB-A96C         TCGA-ZB-A96K         TCGA-3G-AB0O 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-3G-AB0Q         TCGA-3G-AB0T         TCGA-3G-AB14 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-3Q-A9WF         TCGA-3S-A8YW         TCGA-3S-AAYX 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-3T-AA9L         TCGA-4V-A9QI         TCGA-4V-A9QJ 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-4V-A9QL         TCGA-4V-A9QM         TCGA-4V-A9QN 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-4V-A9QQ         TCGA-4V-A9QR         TCGA-4V-A9QS 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-4V-A9QT         TCGA-4V-A9QU         TCGA-4V-A9QW 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-4V-A9QX         TCGA-4X-A9F9         TCGA-4X-A9FA 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-4X-A9FC         TCGA-4X-A9FD         TCGA-5G-A9ZZ 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-5K-AAAP         TCGA-5U-AB0D         TCGA-5U-AB0E 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-5V-A9RR         TCGA-X7-A8D6         TCGA-X7-A8D7 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-X7-A8D8         TCGA-X7-A8D9         TCGA-X7-A8DB 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-X7-A8DC         TCGA-X7-A8DD         TCGA-X7-A8DE 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-X7-A8DF         TCGA-X7-A8DG         TCGA-X7-A8DI 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-X7-A8M0         TCGA-X7-A8M1         TCGA-X7-A8M3 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-X7-A8M4         TCGA-X7-A8M5         TCGA-X7-A8M6 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-X7-A8M8         TCGA-XH-A853         TCGA-XM-A8R8 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XM-A8R9         TCGA-XM-A8RB         TCGA-XM-A8RC 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XM-A8RE         TCGA-XM-A8RF         TCGA-XM-A8RH 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XM-AAZ2         TCGA-XM-AAZ3         TCGA-XU-A92O 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XU-A92R         TCGA-XU-A92T         TCGA-XU-A92U 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XU-A92V         TCGA-XU-A92W         TCGA-XU-A92X 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XU-A92Y         TCGA-XU-A92Z         TCGA-XU-A930 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XU-A931         TCGA-XU-A932         TCGA-XU-A933 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XU-A936         TCGA-XU-AAXW         TCGA-XU-AAXX 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XU-AAXY         TCGA-XU-AAXZ         TCGA-XU-AAY0 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-XU-AAY1         TCGA-YT-A95D         TCGA-YT-A95E 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-YT-A95G         TCGA-YT-A95H         TCGA-ZB-A961 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZB-A962         TCGA-ZB-A963         TCGA-ZB-A964 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZB-A969         TCGA-ZB-A96A         TCGA-ZB-A96B 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZB-A96D         TCGA-ZB-A96F         TCGA-ZB-A96G 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZB-A96H         TCGA-ZB-A96I         TCGA-ZB-A96L 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZB-A96M         TCGA-ZB-A96O         TCGA-ZB-A96Q 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZB-A96R         TCGA-ZB-A96V         TCGA-ZC-AAA7 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZC-AAAA         TCGA-ZC-AAAF         TCGA-ZC-AAAH 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
        TCGA-ZL-A9V6         TCGA-ZT-A8OM 
"PLEKHG4B WILD-TYPE" "PLEKHG4B WILD-TYPE" 
D7V8, binary
                    cls
clus                  0  1
  PLEKHG4B MUTATED    0  2
  PLEKHG4B WILD-TYPE  9 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PLEKHG4B MUTATED      0    2
  PLEKHG4B WILD-TYPE    9   95
                        clus
vv                       PLEKHG4B MUTATED PLEKHG4B WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                2                 95
[1] 2 2
[1] FALSE

Clustering(8) Variable = UNC93B1 MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  UNC93B1 MUTATED     5   0
  UNC93B1 WILD-TYPE 105   9
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                5               114 
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                0                 9 
$`UNC93B1 MUTATED`
TCGA-XM-A8RG TCGA-4V-A9QL TCGA-X7-A8DJ TCGA-XU-A92T TCGA-YT-A95D 
       12.69        62.73         9.50        45.24        24.66 

$`UNC93B1 WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-AAZ1 TCGA-XU-A92Q 
       95.67        23.57        15.09        50.83        13.05        35.90 
TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O TCGA-3G-AB0Q 
       25.48        26.83        71.11        45.63        68.58        59.15 
TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L 
       81.80        25.48        15.35        21.14        18.77        34.52 
TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR 
       96.53        93.67        41.19        31.89        51.68        25.64 
TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 
       25.45        26.73        20.61        20.71        14.27        21.99 
TCGA-4X-A9FA TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D 
       12.89        68.12        49.41        27.45        34.65        23.47 
TCGA-5U-AB0E TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB 
       22.59        27.19       138.90        10.68         1.91        65.49 
TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI 
       59.11        36.62        32.25        29.62        22.85        23.18 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 
       14.50        42.15         1.64       125.19        54.08       150.41 
TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC 
       83.28        40.11        52.54        48.92        37.61        97.41 
TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       13.87        26.20        11.93        12.72        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X 
      112.11        90.05       149.98         4.08       107.80        77.03 
TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 
      114.67       120.43        82.65        52.90        70.65        58.82 
TCGA-XU-A936 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 
       21.14       123.68        89.46        62.17        50.53        49.38 
TCGA-XU-AAY1 TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 
      107.44        35.18        49.78        23.38         5.92        54.15 
TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       48.72        42.31        12.46        34.39        77.39        72.69 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I 
       64.44        59.80        57.90        52.80        49.45        54.35 
TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V 
       50.27         0.46        34.52        22.19        59.31        30.64 
TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       28.04        26.93        38.30        16.34        68.91        45.96 

  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
             9.50              0.46 
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
            62.73            150.41 
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
            24.66             40.65 
[1] "9.5 - 62.7 (24.7)"  "0.5 - 150.4 (40.6)"
[1] "hr="     "2.6e+07"
D8V2, continuous
D8V3, binary
                   cls
clus                 0  1
  UNC93B1 MUTATED    1  4
  UNC93B1 WILD-TYPE 24 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UNC93B1 MUTATED      1    4
  UNC93B1 WILD-TYPE   24   91
                      clus
vv                     UNC93B1 MUTATED UNC93B1 WILD-TYPE
  ANTERIOR MEDIASTINUM               1                24
  THYMUS                             4                91
[1] 2 2
[1] FALSE
D8V4, binary
                   cls
clus                 0  1
  UNC93B1 MUTATED    3  2
  UNC93B1 WILD-TYPE 56 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UNC93B1 MUTATED      3    2
  UNC93B1 WILD-TYPE   56   59
        clus
vv       UNC93B1 MUTATED UNC93B1 WILD-TYPE
  FEMALE               3                56
  MALE                 2                59
[1] 2 2
[1] FALSE
D8V5, binary
                   cls
clus                 0  1
  UNC93B1 MUTATED    5  0
  UNC93B1 WILD-TYPE 73 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UNC93B1 MUTATED      5    0
  UNC93B1 WILD-TYPE   73   42
     clus
vv    UNC93B1 MUTATED UNC93B1 WILD-TYPE
  NO                5                73
  YES               0                42
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  UNC93B1 MUTATED                 1                4                0
  UNC93B1 WILD-TYPE              16               34               13
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  UNC93B1 MUTATED                  0                0               0
  UNC93B1 WILD-TYPE               29               12              11
D8V6, multiclass
                  clus
vv                 UNC93B1 MUTATED UNC93B1 WILD-TYPE
  THYMOMA; TYPE A                1                16
  THYMOMA; TYPE AB               4                34
  THYMOMA; TYPE B1               0                13
  THYMOMA; TYPE B2               0                29
  THYMOMA; TYPE B3               0                12
  THYMOMA; TYPE C                0                11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UNC93B1 MUTATED       0                         0     4
  UNC93B1 WILD-TYPE    13                         6    95
D8V7, multiclass
                           clus
vv                          UNC93B1 MUTATED UNC93B1 WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   4                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                   cls
clus                 0  1
  UNC93B1 MUTATED    1  2
  UNC93B1 WILD-TYPE  8 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UNC93B1 MUTATED      1    2
  UNC93B1 WILD-TYPE    8   95
                        clus
vv                       UNC93B1 MUTATED UNC93B1 WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO               2                95
[1] 2 2
[1] FALSE
