[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/22516316/transformed.cor.cli.txt"

nPatients in clinical file=124, in cluster file=123, common to both=123
[1] "Reduce the number of clustering variables from 82 to 51."
[1]  51 123
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6               117 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6               117 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               23               100 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               23               100 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5               118 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5               118 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11               112 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11               112 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9               114 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9               114 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               16               107 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               16               107 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               16               107 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               16               107 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12               111 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12               111 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               12               111 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               12               111 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               11               112 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               11               112 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               11               112 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               11               112 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                119 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                119 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                119 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                119 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                13                110 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                13                110 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                12                111 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                12                111 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                116 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                116 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                120 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                120 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                120 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                120 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                120 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                120 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                120 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                120 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                10                113 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                10                113 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                113 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                113 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                120 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                120 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                119 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                119 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4               119 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4               119 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5               118 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5               118 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               12               111 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               12               111 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                7               116 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                7               116 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                5               118 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                5               118 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4               119 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4               119 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               21               102 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               21               102 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               20               103 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               20               103 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                4               119 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                4               119 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 3                120 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 3                120 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 9                114 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 9                114 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                116 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                116 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 8                115 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 8                115 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 7                116 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 7                116 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                109 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                109 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                118 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                118 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                13                110 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                13                110 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                14                109 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                14                109 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 6                117 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 6                117 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                116 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                116 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                116 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                116 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                120 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                120 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                120 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                120 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 9                114 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 9                114 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                13                110 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                13                110 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                8               115 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                8               115 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5               118 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5               118 
[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 123 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=49,	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=110,	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 123 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=49, 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 = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED     5   1
  1P GAIN WILD-TYPE 108   8
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6               116 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                 8 
$`1P GAIN MUTATED`
TCGA-3G-AB0T TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-XU-A932 TCGA-YT-A95G TCGA-ZB-A96I 
       81.80        27.45        23.47        70.65        49.78        54.35 

$`1P GAIN 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-AB14 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L 
       59.15        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-5K-AAAP TCGA-5U-AB0E 
       21.99        12.89        68.12        49.41        34.65        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-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       64.83        83.28        40.11        52.54        48.92        37.61 
TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
       97.41        13.87        26.20        11.93        12.72        84.23 
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-A933 TCGA-XU-A936 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY 
       52.90        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-A95H 
       50.53        49.38       107.44        24.66        35.18        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-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       49.45        50.27         0.46        34.52        24.76        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 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            23.47              0.46 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            81.80            150.41 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           52.065            39.205 
[1] "23.5 - 81.8 (52.1)" "0.5 - 150.4 (39.2)"
[1] "hr=" "2.9"
D1V2, continuous
D1V3, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    3  3
  1P GAIN WILD-TYPE 24 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3    3
  1P GAIN WILD-TYPE   24   93
                      clus
vv                     1P GAIN MUTATED 1P GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM               3                24
  THYMUS                             3                93
[1] 2 2
[1] FALSE
D1V4, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    4  2
  1P GAIN WILD-TYPE 55 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4    2
  1P GAIN WILD-TYPE   55   62
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               4                55
  MALE                 2                62
[1] 2 2
[1] FALSE
D1V5, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    4  2
  1P GAIN WILD-TYPE 77 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4    2
  1P GAIN WILD-TYPE   77   40
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                4                77
  YES               2                40
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  1P GAIN MUTATED                 0                1                1
  1P GAIN WILD-TYPE              17               37               14
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  1P GAIN MUTATED                  2                0               2
  1P GAIN WILD-TYPE               28               12               9
D1V6, multiclass
                  clus
vv                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               1                37
  THYMOMA; TYPE B1               1                14
  THYMOMA; TYPE B2               2                28
  THYMOMA; TYPE B3               0                12
  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
  1P GAIN MUTATED       1                         0     5
  1P GAIN WILD-TYPE    12                         6    97
D1V7, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   5                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"
D1V8, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    1  4
  1P GAIN WILD-TYPE  8 96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    4
  1P GAIN WILD-TYPE    8   96
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO               4                96
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   17  6
  1Q GAIN WILD-TYPE 96  3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               23                99 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                6                 3 
$`1Q GAIN MUTATED`
TCGA-XM-A8RD TCGA-XM-AAZ1 TCGA-3G-AB0T TCGA-3S-A8YW TCGA-4V-A9QN TCGA-4V-A9QR 
       50.83        13.05        81.80        21.14        31.89        25.64 
TCGA-4V-A9QS TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-X7-A8M3 TCGA-XU-A92Y 
       25.45        49.41        27.45        23.47         1.64       114.67 
TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A936 TCGA-YT-A95G TCGA-ZB-A961 
       82.65        52.90        70.65        21.14        49.78         5.92 
TCGA-ZB-A966 TCGA-ZB-A96F TCGA-ZB-A96I TCGA-ZB-A96V TCGA-ZC-AAA7 
       12.46        57.90        54.35        30.64        28.04 

$`1Q GAIN WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RG TCGA-XU-A92Q TCGA-YT-A95F 
       95.67        23.57        15.09        12.69        35.90        25.48 
TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB14 
       26.83        71.11        45.63        68.58        59.15        25.48 
TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       15.35        18.77        34.52        96.53        93.67        62.73 
TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       41.19        51.68        26.73        20.61        20.71        14.27 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-5K-AAAP TCGA-5U-AB0E TCGA-5V-A9RR 
       21.99        12.89        68.12        34.65        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-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 
       42.15       125.19        54.08       150.41        64.83        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-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       26.20        11.93        12.72        84.23        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-A92Z TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY 
       77.03       120.43        58.82       123.68        89.46        62.17 
TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95H 
       50.53        49.38       107.44        24.66        35.18        23.38 
TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       54.15        48.72        42.31        34.39        77.39        72.69 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96L TCGA-ZB-A96M 
       64.44        59.80        52.80        49.45        50.27         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZC-AAAA TCGA-ZC-AAAF 
       34.52        24.76        22.19        59.31        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       16.34        68.91        45.96 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             1.64              0.46 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           114.67            150.41 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            30.64             42.15 
[1] "1.6 - 114.7 (30.6)" "0.5 - 150.4 (42.1)"
[1] "hr=" "11" 
D2V2, continuous
D2V3, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    6 17
  1Q GAIN WILD-TYPE 21 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6   17
  1Q GAIN WILD-TYPE   21   79
                      clus
vv                     1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM               6                21
  THYMUS                            17                79
[1] 2 2
[1] FALSE
D2V4, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   14  9
  1Q GAIN WILD-TYPE 45 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     14    9
  1Q GAIN WILD-TYPE   45   55
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              14                45
  MALE                 9                55
[1] 2 2
[1] FALSE
D2V5, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   10 13
  1Q GAIN WILD-TYPE 71 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     10   13
  1Q GAIN WILD-TYPE   71   29
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               10                71
  YES              13                29
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  1Q GAIN MUTATED                 1                2                1
  1Q GAIN WILD-TYPE              16               36               14
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  1Q GAIN MUTATED                  6                6               7
  1Q GAIN WILD-TYPE               24                6               4
D2V6, multiclass
                  clus
vv                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  THYMOMA; TYPE A                1                16
  THYMOMA; TYPE AB               2                36
  THYMOMA; TYPE B1               1                14
  THYMOMA; TYPE B2               6                24
  THYMOMA; TYPE B3               6                 6
  THYMOMA; TYPE C                7                 4
[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
  1Q GAIN MUTATED       1                         0    22
  1Q GAIN WILD-TYPE    12                         6    80
D2V7, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  22                80
[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
  1Q GAIN MUTATED    3 18
  1Q GAIN WILD-TYPE  6 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3   18
  1Q GAIN WILD-TYPE    6   82
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 6
  NOT HISPANIC OR LATINO              18                82
[1] 2 2
[1] FALSE

Clustering(3) Variable = 3Q GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED     3   2
  3Q GAIN WILD-TYPE 110   7
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5               117 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                 7 
$`3Q GAIN MUTATED`
TCGA-4V-A9QJ TCGA-X7-A8M3 TCGA-ZB-A966 TCGA-ZB-A96L TCGA-ZC-AAA7 
       93.67         1.64        12.46        50.27        28.04 

$`3Q GAIN 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-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ 
       34.52        96.53        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-A8M4 TCGA-X7-A8M5 
       23.18         9.50        14.50        42.15       125.19        54.08 
TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      150.41        64.83        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-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       84.23        32.25        37.81       112.11        90.05        45.24 
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-A962 TCGA-ZB-A963 
       35.18        49.78        23.38         5.92        54.15        48.72 
TCGA-ZB-A964 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       42.31        34.39        77.39        72.69        64.44        59.80 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96M TCGA-ZB-A96O 
       57.90        52.80        49.45        54.35         0.46        34.52 
TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAAA TCGA-ZC-AAAF 
       24.76        22.19        59.31        30.64        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       16.34        68.91        45.96 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             1.64              0.46 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            93.67            150.41 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            28.04             41.19 
[1] "1.6 - 93.7 (28.0)"  "0.5 - 150.4 (41.2)"
[1] "hr=" "11" 
D3V2, continuous
D3V3, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    0  5
  3Q GAIN WILD-TYPE 27 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0    5
  3Q GAIN WILD-TYPE   27   91
                      clus
vv                     3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM               0                27
  THYMUS                             5                91
[1] 2 2
[1] FALSE
D3V4, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    3  2
  3Q GAIN WILD-TYPE 56 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    2
  3Q GAIN WILD-TYPE   56   62
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               3                56
  MALE                 2                62
[1] 2 2
[1] FALSE
D3V5, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    3  2
  3Q GAIN WILD-TYPE 78 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    2
  3Q GAIN WILD-TYPE   78   40
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                3                78
  YES               2                40
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  3Q GAIN MUTATED                 0                0                0
  3Q GAIN WILD-TYPE              17               38               15
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  3Q GAIN MUTATED                  0                3               2
  3Q GAIN WILD-TYPE               30                9               9
D3V6, multiclass
                  clus
vv                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               0                38
  THYMOMA; TYPE B1               0                15
  THYMOMA; TYPE B2               0                30
  THYMOMA; TYPE B3               3                 9
  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
  3Q GAIN MUTATED       0                         0     5
  3Q GAIN WILD-TYPE    13                         6    97
D3V7, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   5                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"
D3V8, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    0  5
  3Q GAIN WILD-TYPE  9 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0    5
  3Q GAIN WILD-TYPE    9   95
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               5                95
[1] 2 2
[1] FALSE

Clustering(4) Variable = 5P GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED     9   2
  5P GAIN WILD-TYPE 104   7
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11               111 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                 7 
$`5P GAIN MUTATED`
TCGA-XM-AAZ1 TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4V-A9QS TCGA-5U-AB0D TCGA-X7-A8M3 
       13.05        31.89        25.64        25.45        23.47         1.64 
TCGA-XM-A8RC TCGA-XM-A8RI TCGA-XU-A92Y TCGA-XU-A931 TCGA-XU-A936 
       97.41        12.72       114.67        52.90        21.14 

$`5P GAIN 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-A9QQ TCGA-4V-A9QT 
       96.53        93.67        62.73        41.19        51.68        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-AB0E TCGA-5V-A9RR TCGA-X7-A8D6 
       49.41        27.45        34.65        22.59        27.19       138.90 
TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE 
       10.68         1.91        65.49        59.11        36.62        32.25 
TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 
       29.62        22.85        23.18         9.50        14.50        42.15 
TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 
      125.19        54.08       150.41        64.83        83.28        40.11 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH 
       52.54        48.92        37.61        13.87        26.20        11.93 
TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       84.23        32.25        37.81       112.11        90.05        45.24 
TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Z TCGA-XU-A930 
      149.98         4.08       107.80        77.03       120.43        82.65 
TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ 
       70.65        58.82       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-A96P 
       49.45        54.35        50.27         0.46        34.52        24.76 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
       22.19        59.31        30.64        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       16.34        68.91        45.96 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             1.64              0.46 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           114.67            150.41 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            25.45             42.31 
[1] "1.6 - 114.7 (25.4)" "0.5 - 150.4 (42.3)"
[1] "hr=" "2.9"
D4V2, continuous
D4V3, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    5  6
  5P GAIN WILD-TYPE 22 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      5    6
  5P GAIN WILD-TYPE   22   90
                      clus
vv                     5P GAIN MUTATED 5P GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM               5                22
  THYMUS                             6                90
[1] 2 2
[1] FALSE
D4V4, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    8  3
  5P GAIN WILD-TYPE 51 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      8    3
  5P GAIN WILD-TYPE   51   61
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               8                51
  MALE                 3                61
[1] 2 2
[1] FALSE
D4V5, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    4  7
  5P GAIN WILD-TYPE 77 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4    7
  5P GAIN WILD-TYPE   77   35
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                4                77
  YES               7                35
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  5P GAIN MUTATED                 0                0                0
  5P GAIN WILD-TYPE              17               38               15
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  5P GAIN MUTATED                  4                5               2
  5P GAIN WILD-TYPE               26                7               9
D4V6, multiclass
                  clus
vv                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               0                38
  THYMOMA; TYPE B1               0                15
  THYMOMA; TYPE B2               4                26
  THYMOMA; TYPE B3               5                 7
  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
  5P GAIN MUTATED       0                         0    10
  5P GAIN WILD-TYPE    13                         6    92
D4V7, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  10                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    2  7
  5P GAIN WILD-TYPE  7 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2    7
  5P GAIN WILD-TYPE    7   93
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO               7                93
[1] 2 2
[1] FALSE

Clustering(5) Variable = 5Q GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED     7   2
  5Q GAIN WILD-TYPE 106   7
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9               113 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                 7 
$`5Q GAIN MUTATED`
TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4V-A9QS TCGA-X7-A8M3 TCGA-XM-A8RC TCGA-XM-A8RI 
       31.89        25.64        25.45         1.64        97.41        12.72 
TCGA-XU-A92Y TCGA-XU-A931 TCGA-XU-A936 
      114.67        52.90        21.14 

$`5Q GAIN 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-A9QQ 
       34.52        96.53        93.67        62.73        41.19        51.68 
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-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 
       14.50        42.15       125.19        54.08       150.41        64.83 
TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE 
       83.28        40.11        52.54        48.92        37.61        13.87 
TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O 
       26.20        11.93        84.23        32.25        37.81       112.11 
TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X 
       90.05        45.24       149.98         4.08       107.80        77.03 
TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX 
      120.43        82.65        70.65        58.82       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-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46        34.39        77.39        72.69        64.44        59.80 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M 
       57.90        52.80        49.45        54.35        50.27         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
       34.52        24.76        22.19        59.31        30.64        28.04 
TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       26.93        38.30        16.34        68.91        45.96 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             1.64              0.46 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           114.67            150.41 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            25.64             42.15 
[1] "1.6 - 114.7 (25.6)" "0.5 - 150.4 (42.1)"
[1] "hr=" "3.1"
D5V2, continuous
D5V3, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    3  6
  5Q GAIN WILD-TYPE 24 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3    6
  5Q GAIN WILD-TYPE   24   90
                      clus
vv                     5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM               3                24
  THYMUS                             6                90
[1] 2 2
[1] FALSE
D5V4, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    7  2
  5Q GAIN WILD-TYPE 52 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7    2
  5Q GAIN WILD-TYPE   52   62
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               7                52
  MALE                 2                62
[1] 2 2
[1] FALSE
D5V5, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    3  6
  5Q GAIN WILD-TYPE 78 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3    6
  5Q GAIN WILD-TYPE   78   36
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                3                78
  YES               6                36
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  5Q GAIN MUTATED                 0                0                0
  5Q GAIN WILD-TYPE              17               38               15
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  5Q GAIN MUTATED                  3                5               1
  5Q GAIN WILD-TYPE               27                7              10
D5V6, multiclass
                  clus
vv                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               0                38
  THYMOMA; TYPE B1               0                15
  THYMOMA; TYPE B2               3                27
  THYMOMA; TYPE B3               5                 7
  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
  5Q GAIN MUTATED       0                         0     8
  5Q GAIN WILD-TYPE    13                         6    94
D5V7, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   8                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    1  6
  5Q GAIN WILD-TYPE  8 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1    6
  5Q GAIN WILD-TYPE    8   94
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO               6                94
[1] 2 2
[1] FALSE

Clustering(6) Variable = 7P GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    13   3
  7P GAIN WILD-TYPE 100   6
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               16               106 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                3                 6 
$`7P GAIN MUTATED`
TCGA-XM-A8RD TCGA-XM-AAZ1 TCGA-3G-AB0T TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4X-A9FD 
       50.83        13.05        81.80        25.64        25.45        49.41 
TCGA-5U-AB0E TCGA-X7-A8M3 TCGA-XM-A8RC TCGA-XM-A8RI TCGA-XU-A92X TCGA-XU-A92Y 
       22.59         1.64        97.41        12.72        77.03       114.67 
TCGA-XU-A930 TCGA-XU-A931 TCGA-ZB-A96F TCGA-ZB-A96I 
       82.65        52.90        57.90        54.35 

$`7P GAIN WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RG TCGA-XU-A92Q TCGA-YT-A95F 
       95.67        23.57        15.09        12.69        35.90        25.48 
TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB14 
       26.83        71.11        45.63        68.58        59.15        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-A9QT TCGA-4V-A9QU 
       62.73        41.19        31.89        51.68        26.73        20.61 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-5G-A9ZZ 
       20.71        14.27        21.99        12.89        68.12        27.45 
TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 
       34.65        23.47        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-A8M4 TCGA-X7-A8M5 
       23.18         9.50        14.50        42.15       125.19        54.08 
TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      150.41        64.83        83.28        40.11        52.54        48.92 
TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RL TCGA-XM-AAZ2 
       37.61        13.87        26.20        11.93        84.23        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
       37.81       112.11        90.05        45.24       149.98         4.08 
TCGA-XU-A92W TCGA-XU-A92Z TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXW 
      107.80       120.43        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-A962 TCGA-ZB-A963 
       35.18        49.78        23.38         5.92        54.15        48.72 
TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D 
       42.31        12.46        34.39        77.39        72.69        64.44 
TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O 
       59.80        52.80        49.45        50.27         0.46        34.52 
TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       24.76        22.19        59.31        30.64        28.04        26.93 
TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       38.30        16.34        68.91        45.96 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             1.64              0.46 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           114.67            150.41 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           51.865            38.055 
[1] "1.6 - 114.7 (51.9)" "0.5 - 150.4 (38.1)"
[1] "hr=" "2.9"
D6V2, continuous
D6V3, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    6 10
  7P GAIN WILD-TYPE 21 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      6   10
  7P GAIN WILD-TYPE   21   86
                      clus
vv                     7P GAIN MUTATED 7P GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM               6                21
  THYMUS                            10                86
[1] 2 2
[1] FALSE
D6V4, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    8  8
  7P GAIN WILD-TYPE 51 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      8    8
  7P GAIN WILD-TYPE   51   56
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               8                51
  MALE                 8                56
[1] 2 2
[1] FALSE
D6V5, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    8  8
  7P GAIN WILD-TYPE 73 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      8    8
  7P GAIN WILD-TYPE   73   34
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                8                73
  YES               8                34
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  7P GAIN MUTATED                 0                2                1
  7P GAIN WILD-TYPE              17               36               14
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  7P GAIN MUTATED                  7                6               0
  7P GAIN WILD-TYPE               23                6              11
D6V6, multiclass
                  clus
vv                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               2                36
  THYMOMA; TYPE B1               1                14
  THYMOMA; TYPE B2               7                23
  THYMOMA; TYPE B3               6                 6
  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
  7P GAIN MUTATED       1                         0    14
  7P GAIN WILD-TYPE    12                         6    88
D6V7, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  14                88
[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
  7P GAIN MUTATED    1 13
  7P GAIN WILD-TYPE  8 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      1   13
  7P GAIN WILD-TYPE    8   87
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              13                87
[1] 2 2
[1] FALSE

Clustering(7) Variable = 7Q GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    13   3
  7Q GAIN WILD-TYPE 100   6
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               16               106 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                3                 6 
$`7Q GAIN MUTATED`
TCGA-XM-A8RD TCGA-XM-AAZ1 TCGA-3G-AB0T TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4X-A9FD 
       50.83        13.05        81.80        25.64        25.45        49.41 
TCGA-5U-AB0E TCGA-X7-A8M3 TCGA-XM-A8RC TCGA-XM-A8RI TCGA-XU-A92X TCGA-XU-A92Y 
       22.59         1.64        97.41        12.72        77.03       114.67 
TCGA-XU-A930 TCGA-XU-A931 TCGA-ZB-A96F TCGA-ZB-A96I 
       82.65        52.90        57.90        54.35 

$`7Q GAIN WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RG TCGA-XU-A92Q TCGA-YT-A95F 
       95.67        23.57        15.09        12.69        35.90        25.48 
TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB14 
       26.83        71.11        45.63        68.58        59.15        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-A9QT TCGA-4V-A9QU 
       62.73        41.19        31.89        51.68        26.73        20.61 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-5G-A9ZZ 
       20.71        14.27        21.99        12.89        68.12        27.45 
TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 
       34.65        23.47        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-A8M4 TCGA-X7-A8M5 
       23.18         9.50        14.50        42.15       125.19        54.08 
TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      150.41        64.83        83.28        40.11        52.54        48.92 
TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RL TCGA-XM-AAZ2 
       37.61        13.87        26.20        11.93        84.23        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
       37.81       112.11        90.05        45.24       149.98         4.08 
TCGA-XU-A92W TCGA-XU-A92Z TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXW 
      107.80       120.43        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-A962 TCGA-ZB-A963 
       35.18        49.78        23.38         5.92        54.15        48.72 
TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D 
       42.31        12.46        34.39        77.39        72.69        64.44 
TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O 
       59.80        52.80        49.45        50.27         0.46        34.52 
TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       24.76        22.19        59.31        30.64        28.04        26.93 
TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       38.30        16.34        68.91        45.96 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             1.64              0.46 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           114.67            150.41 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           51.865            38.055 
[1] "1.6 - 114.7 (51.9)" "0.5 - 150.4 (38.1)"
[1] "hr=" "2.9"
D7V2, continuous
D7V3, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    6 10
  7Q GAIN WILD-TYPE 21 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      6   10
  7Q GAIN WILD-TYPE   21   86
                      clus
vv                     7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM               6                21
  THYMUS                            10                86
[1] 2 2
[1] FALSE
D7V4, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    8  8
  7Q GAIN WILD-TYPE 51 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      8    8
  7Q GAIN WILD-TYPE   51   56
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               8                51
  MALE                 8                56
[1] 2 2
[1] FALSE
D7V5, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    8  8
  7Q GAIN WILD-TYPE 73 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      8    8
  7Q GAIN WILD-TYPE   73   34
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                8                73
  YES               8                34
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  7Q GAIN MUTATED                 0                2                1
  7Q GAIN WILD-TYPE              17               36               14
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  7Q GAIN MUTATED                  7                6               0
  7Q GAIN WILD-TYPE               23                6              11
D7V6, multiclass
                  clus
vv                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               2                36
  THYMOMA; TYPE B1               1                14
  THYMOMA; TYPE B2               7                23
  THYMOMA; TYPE B3               6                 6
  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
  7Q GAIN MUTATED       1                         0    14
  7Q GAIN WILD-TYPE    12                         6    88
D7V7, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  14                88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    1 13
  7Q GAIN WILD-TYPE  8 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      1   13
  7Q GAIN WILD-TYPE    8   87
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              13                87
[1] 2 2
[1] FALSE

Clustering(8) Variable = 8P GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    10   2
  8P GAIN WILD-TYPE 103   7
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12               110 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                 7 
$`8P GAIN MUTATED`
TCGA-XM-AAZ1 TCGA-3G-AB0T TCGA-3S-A8YW TCGA-X7-A8M3 TCGA-XM-A8RB TCGA-XM-A8RC 
       13.05        81.80        21.14         1.64        37.61        97.41 
TCGA-XU-A932 TCGA-XU-A936 TCGA-YT-A95G TCGA-ZB-A96F TCGA-ZB-A96V TCGA-ZC-AAA7 
       70.65        21.14        49.78        57.90        30.64        28.04 

$`8P GAIN 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-AB14 TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ 
       25.48        15.35        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-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-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 
       14.50        42.15       125.19        54.08       150.41        64.83 
TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RE TCGA-XM-A8RF 
       83.28        40.11        52.54        48.92        13.87        26.20 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O 
       11.93        12.72        84.23        32.25        37.81       112.11 
TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X 
       90.05        45.24       149.98         4.08       107.80        77.03 
TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A933 TCGA-XU-AAXW 
      114.67       120.43        82.65        52.90        58.82       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-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       35.18        23.38         5.92        54.15        48.72        42.31 
TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46        34.39        77.39        72.69        64.44        59.80 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O 
       52.80        49.45        54.35        50.27         0.46        34.52 
TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
       24.76        22.19        59.31        26.93        38.30        16.34 
TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       68.91        45.96 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             1.64              0.46 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            97.41            150.41 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           34.125            41.670 
[1] "1.6 - 97.4 (34.1)"  "0.5 - 150.4 (41.7)"
[1] "hr=" "3.2"
D8V2, continuous
D8V3, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    4  8
  8P GAIN WILD-TYPE 23 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4    8
  8P GAIN WILD-TYPE   23   88
                      clus
vv                     8P GAIN MUTATED 8P GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM               4                23
  THYMUS                             8                88
[1] 2 2
[1] FALSE
D8V4, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    4  8
  8P GAIN WILD-TYPE 55 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4    8
  8P GAIN WILD-TYPE   55   56
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               4                55
  MALE                 8                56
[1] 2 2
[1] FALSE
D8V5, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    6  6
  8P GAIN WILD-TYPE 75 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      6    6
  8P GAIN WILD-TYPE   75   36
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                6                75
  YES               6                36
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  8P GAIN MUTATED                 0                1                2
  8P GAIN WILD-TYPE              17               37               13
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  8P GAIN MUTATED                  4                1               4
  8P GAIN WILD-TYPE               26               11               7
D8V6, multiclass
                  clus
vv                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               1                37
  THYMOMA; TYPE B1               2                13
  THYMOMA; TYPE B2               4                26
  THYMOMA; TYPE B3               1                11
  THYMOMA; TYPE C                4                 7
[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
  8P GAIN MUTATED       1                         1    10
  8P GAIN WILD-TYPE    12                         5    92
D8V7, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                  10                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    1 10
  8P GAIN WILD-TYPE  8 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   10
  8P GAIN WILD-TYPE    8   90
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              10                90
[1] 2 2
[1] FALSE

Clustering(9) Variable = 8Q GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    10   2
  8Q GAIN WILD-TYPE 103   7
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               12               110 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                 7 
$`8Q GAIN MUTATED`
TCGA-XM-AAZ1 TCGA-3G-AB0T TCGA-3S-A8YW TCGA-X7-A8M3 TCGA-XM-A8RB TCGA-XM-A8RC 
       13.05        81.80        21.14         1.64        37.61        97.41 
TCGA-XU-A932 TCGA-XU-A936 TCGA-YT-A95G TCGA-ZB-A96F TCGA-ZB-A96V TCGA-ZC-AAA7 
       70.65        21.14        49.78        57.90        30.64        28.04 

$`8Q GAIN 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-AB14 TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ 
       25.48        15.35        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-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-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 
       14.50        42.15       125.19        54.08       150.41        64.83 
TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RE TCGA-XM-A8RF 
       83.28        40.11        52.54        48.92        13.87        26.20 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O 
       11.93        12.72        84.23        32.25        37.81       112.11 
TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X 
       90.05        45.24       149.98         4.08       107.80        77.03 
TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A933 TCGA-XU-AAXW 
      114.67       120.43        82.65        52.90        58.82       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-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       35.18        23.38         5.92        54.15        48.72        42.31 
TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46        34.39        77.39        72.69        64.44        59.80 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O 
       52.80        49.45        54.35        50.27         0.46        34.52 
TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
       24.76        22.19        59.31        26.93        38.30        16.34 
TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       68.91        45.96 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             1.64              0.46 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            97.41            150.41 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           34.125            41.670 
[1] "1.6 - 97.4 (34.1)"  "0.5 - 150.4 (41.7)"
[1] "hr=" "3.2"
D9V2, continuous
D9V3, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    4  8
  8Q GAIN WILD-TYPE 23 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      4    8
  8Q GAIN WILD-TYPE   23   88
                      clus
vv                     8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM               4                23
  THYMUS                             8                88
[1] 2 2
[1] FALSE
D9V4, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    4  8
  8Q GAIN WILD-TYPE 55 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      4    8
  8Q GAIN WILD-TYPE   55   56
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               4                55
  MALE                 8                56
[1] 2 2
[1] FALSE
D9V5, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    6  6
  8Q GAIN WILD-TYPE 75 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6    6
  8Q GAIN WILD-TYPE   75   36
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                6                75
  YES               6                36
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  8Q GAIN MUTATED                 0                1                2
  8Q GAIN WILD-TYPE              17               37               13
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  8Q GAIN MUTATED                  4                1               4
  8Q GAIN WILD-TYPE               26               11               7
D9V6, multiclass
                  clus
vv                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               1                37
  THYMOMA; TYPE B1               2                13
  THYMOMA; TYPE B2               4                26
  THYMOMA; TYPE B3               1                11
  THYMOMA; TYPE C                4                 7
[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
  8Q GAIN MUTATED       1                         1    10
  8Q GAIN WILD-TYPE    12                         5    92
D9V7, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                  10                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    1 10
  8Q GAIN WILD-TYPE  8 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   10
  8Q GAIN WILD-TYPE    8   90
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              10                90
[1] 2 2
[1] FALSE

Clustering(10) Variable = 9P GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     9   2
  9P GAIN WILD-TYPE 104   7
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               11               111 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                 7 
$`9P GAIN MUTATED`
TCGA-XM-AAZ1 TCGA-3G-AB0T TCGA-4V-A9QR TCGA-4V-A9QS TCGA-XU-A92R TCGA-XU-A92X 
       13.05        81.80        25.64        25.45        90.05        77.03 
TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-AAXW TCGA-ZB-A96F 
       82.65        52.90        70.65       123.68        57.90 

$`9P GAIN 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-AB14 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI 
       25.48        15.35        21.14        18.77        34.52        96.53 
TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QT 
       93.67        62.73        41.19        31.89        51.68        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-A8M7 
       42.15         1.64       125.19        54.08       150.41        64.83 
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-A8RL TCGA-XM-AAZ2 
       13.87        26.20        11.93        12.72        84.23        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W 
       37.81       112.11        45.24       149.98         4.08       107.80 
TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXX TCGA-XU-AAXY 
      114.67       120.43        58.82        21.14        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-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G 
       34.39        77.39        72.69        64.44        59.80        52.80 
TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
       49.45        54.35        50.27         0.46        34.52        24.76 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
       22.19        59.31        30.64        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       16.34        68.91        45.96 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            13.05              0.46 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           123.68            150.41 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            70.65             37.81 
[1] "13.1 - 123.7 (70.7)" "0.5 - 150.4 (37.8)" 
[1] "hr=" "2.1"
D10V2, continuous
D10V3, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    2  9
  9P GAIN WILD-TYPE 25 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    9
  9P GAIN WILD-TYPE   25   87
                      clus
vv                     9P GAIN MUTATED 9P GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM               2                25
  THYMUS                             9                87
[1] 2 2
[1] FALSE
D10V4, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    5  6
  9P GAIN WILD-TYPE 54 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      5    6
  9P GAIN WILD-TYPE   54   58
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               5                54
  MALE                 6                58
[1] 2 2
[1] FALSE
D10V5, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    3  8
  9P GAIN WILD-TYPE 78 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    8
  9P GAIN WILD-TYPE   78   34
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                3                78
  YES               8                34
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  9P GAIN MUTATED                 0                2                1
  9P GAIN WILD-TYPE              17               36               14
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  9P GAIN MUTATED                  5                3               0
  9P GAIN WILD-TYPE               25                9              11
D10V6, multiclass
                  clus
vv                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               2                36
  THYMOMA; TYPE B1               1                14
  THYMOMA; TYPE B2               5                25
  THYMOMA; TYPE B3               3                 9
  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
  9P GAIN MUTATED       4                         0     7
  9P GAIN WILD-TYPE     9                         6    95
D10V7, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   4                 9
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   7                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"
D10V8, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    0 10
  9P GAIN WILD-TYPE  9 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   10
  9P GAIN WILD-TYPE    9   90
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              10                90
[1] 2 2
[1] FALSE

Clustering(11) Variable = 9Q GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     9   2
  9Q GAIN WILD-TYPE 104   7
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               11               111 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                 7 
$`9Q GAIN MUTATED`
TCGA-XM-AAZ1 TCGA-3G-AB0T TCGA-4V-A9QR TCGA-4V-A9QS TCGA-XU-A92R TCGA-XU-A92X 
       13.05        81.80        25.64        25.45        90.05        77.03 
TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-AAXW TCGA-ZB-A96F 
       82.65        52.90        70.65       123.68        57.90 

$`9Q GAIN 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-AB14 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI 
       25.48        15.35        21.14        18.77        34.52        96.53 
TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QT 
       93.67        62.73        41.19        31.89        51.68        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-A8M7 
       42.15         1.64       125.19        54.08       150.41        64.83 
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-A8RL TCGA-XM-AAZ2 
       13.87        26.20        11.93        12.72        84.23        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W 
       37.81       112.11        45.24       149.98         4.08       107.80 
TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXX TCGA-XU-AAXY 
      114.67       120.43        58.82        21.14        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-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G 
       34.39        77.39        72.69        64.44        59.80        52.80 
TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
       49.45        54.35        50.27         0.46        34.52        24.76 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
       22.19        59.31        30.64        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       16.34        68.91        45.96 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            13.05              0.46 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           123.68            150.41 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            70.65             37.81 
[1] "13.1 - 123.7 (70.7)" "0.5 - 150.4 (37.8)" 
[1] "hr=" "2.1"
D11V2, continuous
D11V3, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    2  9
  9Q GAIN WILD-TYPE 25 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    9
  9Q GAIN WILD-TYPE   25   87
                      clus
vv                     9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM               2                25
  THYMUS                             9                87
[1] 2 2
[1] FALSE
D11V4, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    5  6
  9Q GAIN WILD-TYPE 54 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      5    6
  9Q GAIN WILD-TYPE   54   58
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               5                54
  MALE                 6                58
[1] 2 2
[1] FALSE
D11V5, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    3  8
  9Q GAIN WILD-TYPE 78 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    8
  9Q GAIN WILD-TYPE   78   34
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                3                78
  YES               8                34
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  9Q GAIN MUTATED                 0                2                1
  9Q GAIN WILD-TYPE              17               36               14
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  9Q GAIN MUTATED                  5                3               0
  9Q GAIN WILD-TYPE               25                9              11
D11V6, multiclass
                  clus
vv                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               2                36
  THYMOMA; TYPE B1               1                14
  THYMOMA; TYPE B2               5                25
  THYMOMA; TYPE B3               3                 9
  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
  9Q GAIN MUTATED       4                         0     7
  9Q GAIN WILD-TYPE     9                         6    95
D11V7, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   4                 9
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   7                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"
D11V8, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    0 10
  9Q GAIN WILD-TYPE  9 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   10
  9Q GAIN WILD-TYPE    9   90
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              10                90
[1] 2 2
[1] FALSE

Clustering(12) Variable = 12P GAIN MUTATION ANALYSIS
D12V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED     3   1
  12P GAIN WILD-TYPE 110   8
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                118 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 1                  8 
$`12P GAIN MUTATED`
TCGA-3S-A8YW TCGA-XM-A8RC TCGA-XU-A936 TCGA-ZC-AAA7 
       21.14        97.41        21.14        28.04 

$`12P GAIN 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-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        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-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
       54.08       150.41        64.83        83.28        40.11        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI 
       48.92        37.61        13.87        26.20        11.93        12.72 
TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       84.23        32.25        37.81       112.11        90.05        45.24 
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-AAXW TCGA-XU-AAXX 
       82.65        52.90        70.65        58.82       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-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46        34.39        77.39        72.69        64.44        59.80 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M 
       57.90        52.80        49.45        54.35        50.27         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAAA 
       34.52        24.76        22.19        59.31        30.64        26.93 
TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       38.30        16.34        68.91        45.96 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             21.14               0.46 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             97.41             150.41 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             24.59              41.67 
[1] "21.1 - 97.4 (24.6)" "0.5 - 150.4 (41.7)"
[1] "hr=" "3.7"
D12V2, continuous
D12V3, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    2  2
  12P GAIN WILD-TYPE 25 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2    2
  12P GAIN WILD-TYPE   25   94
                      clus
vv                     12P GAIN MUTATED 12P GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM                2                 25
  THYMUS                              2                 94
[1] 2 2
[1] FALSE
D12V4, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    1  3
  12P GAIN WILD-TYPE 58 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1    3
  12P GAIN WILD-TYPE   58   61
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                1                 58
  MALE                  3                 61
[1] 2 2
[1] FALSE
D12V5, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    2  2
  12P GAIN WILD-TYPE 79 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2    2
  12P GAIN WILD-TYPE   79   40
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 2                 79
  YES                2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  12P GAIN MUTATED                 0                0                0
  12P GAIN WILD-TYPE              17               38               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  12P GAIN MUTATED                  1                0               3
  12P GAIN WILD-TYPE               29               12               8
D12V6, multiclass
                  clus
vv                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                0                 38
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                1                 29
  THYMOMA; TYPE B3                0                 12
  THYMOMA; TYPE C                 3                  8
[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
  12P GAIN MUTATED       0                         0     4
  12P GAIN WILD-TYPE    13                         6    98
D12V7, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    4                 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"
D12V8, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    1  3
  12P GAIN WILD-TYPE  8 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1    3
  12P GAIN WILD-TYPE    8   97
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO                3                 97
[1] 2 2
[1] FALSE

Clustering(13) Variable = 12Q GAIN MUTATION ANALYSIS
D13V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED     3   1
  12Q GAIN WILD-TYPE 110   8
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                118 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 1                  8 
$`12Q GAIN MUTATED`
TCGA-3S-A8YW TCGA-XM-A8RC TCGA-XU-A936 TCGA-ZC-AAA7 
       21.14        97.41        21.14        28.04 

$`12Q GAIN 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-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        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-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
       54.08       150.41        64.83        83.28        40.11        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI 
       48.92        37.61        13.87        26.20        11.93        12.72 
TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       84.23        32.25        37.81       112.11        90.05        45.24 
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-AAXW TCGA-XU-AAXX 
       82.65        52.90        70.65        58.82       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-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46        34.39        77.39        72.69        64.44        59.80 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M 
       57.90        52.80        49.45        54.35        50.27         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAAA 
       34.52        24.76        22.19        59.31        30.64        26.93 
TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       38.30        16.34        68.91        45.96 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             21.14               0.46 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             97.41             150.41 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             24.59              41.67 
[1] "21.1 - 97.4 (24.6)" "0.5 - 150.4 (41.7)"
[1] "hr=" "3.7"
D13V2, continuous
D13V3, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    2  2
  12Q GAIN WILD-TYPE 25 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2    2
  12Q GAIN WILD-TYPE   25   94
                      clus
vv                     12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM                2                 25
  THYMUS                              2                 94
[1] 2 2
[1] FALSE
D13V4, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    1  3
  12Q GAIN WILD-TYPE 58 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    3
  12Q GAIN WILD-TYPE   58   61
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                1                 58
  MALE                  3                 61
[1] 2 2
[1] FALSE
D13V5, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    2  2
  12Q GAIN WILD-TYPE 79 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2    2
  12Q GAIN WILD-TYPE   79   40
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 2                 79
  YES                2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  12Q GAIN MUTATED                 0                0                0
  12Q GAIN WILD-TYPE              17               38               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  12Q GAIN MUTATED                  1                0               3
  12Q GAIN WILD-TYPE               29               12               8
D13V6, multiclass
                  clus
vv                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                0                 38
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                1                 29
  THYMOMA; TYPE B3                0                 12
  THYMOMA; TYPE C                 3                  8
[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
  12Q GAIN MUTATED       0                         0     4
  12Q GAIN WILD-TYPE    13                         6    98
D13V7, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    4                 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"
D13V8, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    1  3
  12Q GAIN WILD-TYPE  8 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    3
  12Q GAIN WILD-TYPE    8   97
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO                3                 97
[1] 2 2
[1] FALSE

Clustering(14) Variable = 14Q GAIN MUTATION ANALYSIS
D14V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    11   2
  14Q GAIN WILD-TYPE 102   7
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                13                109 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                  7 
$`14Q GAIN MUTATED`
TCGA-XM-AAZ1 TCGA-3G-AB0T TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4X-A9FD TCGA-X7-A8M3 
       13.05        81.80        25.64        25.45        49.41         1.64 
TCGA-XM-A8RC TCGA-XM-A8RI TCGA-XU-A92X TCGA-XU-A931 TCGA-XU-AAXW TCGA-XU-AAXX 
       97.41        12.72        77.03        52.90       123.68        89.46 
TCGA-ZB-A96F 
       57.90 

$`14Q GAIN 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-AB14 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI 
       25.48        15.35        21.14        18.77        34.52        96.53 
TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QT 
       93.67        62.73        41.19        31.89        51.68        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-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5V-A9RR TCGA-X7-A8D6 
       27.45        34.65        23.47        22.59        27.19       138.90 
TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE 
       10.68         1.91        65.49        59.11        36.62        32.25 
TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 
       29.62        22.85        23.18         9.50        14.50        42.15 
TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 
      125.19        54.08       150.41        64.83        83.28        40.11 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH 
       52.54        48.92        37.61        13.87        26.20        11.93 
TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       84.23        32.25        37.81       112.11        90.05        45.24 
TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A930 
      149.98         4.08       107.80       114.67       120.43        82.65 
TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 
       70.65        58.82        21.14        62.17        50.53        49.38 
TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 
      107.44        24.66        35.18        49.78        23.38         5.92 
TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A 
       54.15        48.72        42.31        12.46        34.39        77.39 
TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I 
       72.69        64.44        59.80        52.80        49.45        54.35 
TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
       50.27         0.46        34.52        24.76        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 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1.64               0.46 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            123.68             150.41 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              52.9               38.3 
[1] "1.6 - 123.7 (52.9)" "0.5 - 150.4 (38.3)"
[1] "hr=" "1.9"
D14V2, continuous
D14V3, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    3 10
  14Q GAIN WILD-TYPE 24 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      3   10
  14Q GAIN WILD-TYPE   24   86
                      clus
vv                     14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM                3                 24
  THYMUS                             10                 86
[1] 2 2
[1] FALSE
D14V4, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    7  6
  14Q GAIN WILD-TYPE 52 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      7    6
  14Q GAIN WILD-TYPE   52   58
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                7                 52
  MALE                  6                 58
[1] 2 2
[1] FALSE
D14V5, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    6  7
  14Q GAIN WILD-TYPE 75 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      6    7
  14Q GAIN WILD-TYPE   75   35
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 6                 75
  YES                7                 35
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  14Q GAIN MUTATED                 0                1                1
  14Q GAIN WILD-TYPE              17               37               14
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  14Q GAIN MUTATED                  8                3               0
  14Q GAIN WILD-TYPE               22                9              11
D14V6, multiclass
                  clus
vv                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                1                 37
  THYMOMA; TYPE B1                1                 14
  THYMOMA; TYPE B2                8                 22
  THYMOMA; TYPE B3                3                  9
  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
  14Q GAIN MUTATED       2                         0    10
  14Q GAIN WILD-TYPE    11                         6    92
D14V7, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    2                 11
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                   10                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    0 10
  14Q GAIN WILD-TYPE  9 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   10
  14Q GAIN WILD-TYPE    9   90
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               10                 90
[1] 2 2
[1] FALSE

Clustering(15) Variable = 15Q GAIN MUTATION ANALYSIS
D15V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    10   2
  15Q GAIN WILD-TYPE 103   7
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                12                110 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                  7 
$`15Q GAIN MUTATED`
TCGA-3G-AB0T TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-5U-AB0E TCGA-XM-A8RC 
       81.80        51.68        25.64        25.45        22.59        97.41 
TCGA-XM-A8RF TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A936 TCGA-XU-AAXZ TCGA-ZB-A96F 
       26.20        77.03       114.67        21.14        50.53        57.90 

$`15Q GAIN 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-AB14 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L 
       59.15        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-A9QT 
       96.53        93.67        62.73        41.19        31.89        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-5V-A9RR TCGA-X7-A8D6 
       49.41        27.45        34.65        23.47        27.19       138.90 
TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE 
       10.68         1.91        65.49        59.11        36.62        32.25 
TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 
       29.62        22.85        23.18         9.50        14.50        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 
        1.64       125.19        54.08       150.41        64.83        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RH 
       40.11        52.54        48.92        37.61        13.87        11.93 
TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R 
       12.72        84.23        32.25        37.81       112.11        90.05 
TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92Z TCGA-XU-A930 
       45.24       149.98         4.08       107.80       120.43        82.65 
TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY 
       52.90        70.65        58.82       123.68        89.46        62.17 
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-A96G TCGA-ZB-A96H 
       77.39        72.69        64.44        59.80        52.80        49.45 
TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       54.35        50.27         0.46        34.52        24.76        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 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             21.14               0.46 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            114.67             150.41 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            51.105             39.205 
[1] "21.1 - 114.7 (51.1)" "0.5 - 150.4 (39.2)" 
[1] "hr=" "2.1"
D15V2, continuous
D15V3, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    6  6
  15Q GAIN WILD-TYPE 21 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      6    6
  15Q GAIN WILD-TYPE   21   90
                      clus
vv                     15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM                6                 21
  THYMUS                              6                 90
[1] 2 2
[1] FALSE
D15V4, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    6  6
  15Q GAIN WILD-TYPE 53 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      6    6
  15Q GAIN WILD-TYPE   53   58
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                6                 53
  MALE                  6                 58
[1] 2 2
[1] FALSE
D15V5, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    4  8
  15Q GAIN WILD-TYPE 77 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4    8
  15Q GAIN WILD-TYPE   77   34
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 4                 77
  YES                8                 34
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  15Q GAIN MUTATED                 1                1                1
  15Q GAIN WILD-TYPE              16               37               14
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  15Q GAIN MUTATED                  3                5               1
  15Q GAIN WILD-TYPE               27                7              10
D15V6, multiclass
                  clus
vv                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  THYMOMA; TYPE A                 1                 16
  THYMOMA; TYPE AB                1                 37
  THYMOMA; TYPE B1                1                 14
  THYMOMA; TYPE B2                3                 27
  THYMOMA; TYPE B3                5                  7
  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
  15Q GAIN MUTATED       1                         0    11
  15Q GAIN WILD-TYPE    12                         6    91
D15V7, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                   11                 91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    1 11
  15Q GAIN WILD-TYPE  8 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   11
  15Q GAIN WILD-TYPE    8   89
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               11                 89
[1] 2 2
[1] FALSE

Clustering(16) Variable = 17Q GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED     7   0
  17Q GAIN WILD-TYPE 106   9
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                115 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 0                  9 
$`17Q GAIN MUTATED`
TCGA-XM-A8RG TCGA-4V-A9QJ TCGA-5G-A9ZZ TCGA-XM-A8RC TCGA-XU-A933 TCGA-XU-A936 
       12.69        93.67        27.45        97.41        58.82        21.14 
TCGA-ZB-A962 
       54.15 

$`17Q GAIN 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-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR 
       96.53        62.73        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-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E 
       12.89        68.12        49.41        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-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       64.83        83.28        40.11        52.54        48.92        37.61 
TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 
       13.87        26.20        11.93        12.72        84.23        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
       37.81       112.11        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-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 
       70.65       123.68        89.46        62.17        50.53        49.38 
TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 
      107.44        24.66        35.18        49.78        23.38         5.92 
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-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
       50.27         0.46        34.52        24.76        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 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             12.69               0.46 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             97.41             150.41 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             54.15              40.11 
[1] "12.7 - 97.4 (54.1)" "0.5 - 150.4 (40.1)"
[1] "hr="     "7.4e+07"
D16V2, continuous
D16V3, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    2  5
  17Q GAIN WILD-TYPE 25 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2    5
  17Q GAIN WILD-TYPE   25   91
                      clus
vv                     17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM                2                 25
  THYMUS                              5                 91
[1] 2 2
[1] FALSE
D16V4, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    3  4
  17Q GAIN WILD-TYPE 56 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3    4
  17Q GAIN WILD-TYPE   56   60
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                3                 56
  MALE                  4                 60
[1] 2 2
[1] FALSE
D16V5, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    3  4
  17Q GAIN WILD-TYPE 78 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3    4
  17Q GAIN WILD-TYPE   78   38
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 3                 78
  YES                4                 38
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  17Q GAIN MUTATED                 2                0                0
  17Q GAIN WILD-TYPE              15               38               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  17Q GAIN MUTATED                  1                1               3
  17Q GAIN WILD-TYPE               29               11               8
D16V6, multiclass
                  clus
vv                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  THYMOMA; TYPE A                 2                 15
  THYMOMA; TYPE AB                0                 38
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                1                 29
  THYMOMA; TYPE B3                1                 11
  THYMOMA; TYPE C                 3                  8
[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
  17Q GAIN MUTATED       1                         0     6
  17Q GAIN WILD-TYPE    12                         6    96
D16V7, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    6                 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"
D16V8, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    0  7
  17Q GAIN WILD-TYPE  9 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0    7
  17Q GAIN WILD-TYPE    9   93
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                7                 93
[1] 2 2
[1] FALSE

Clustering(17) Variable = 18P GAIN MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED     3   0
  18P GAIN WILD-TYPE 110   9
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                119 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                  9 
$`18P GAIN MUTATED`
TCGA-3S-A8YW TCGA-XU-A936 TCGA-ZB-A96F 
       21.14        21.14        57.90 

$`18P GAIN 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-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        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-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
       54.08       150.41        64.83        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-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R 
       12.72        84.23        32.25        37.81       112.11        90.05 
TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y 
       45.24       149.98         4.08       107.80        77.03       114.67 
TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW 
      120.43        82.65        52.90        70.65        58.82       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-A962 TCGA-ZB-A963 
       35.18        49.78        23.38         5.92        54.15        48.72 
TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D 
       42.31        12.46        34.39        77.39        72.69        64.44 
TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M 
       59.80        52.80        49.45        54.35        50.27         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
       34.52        24.76        22.19        59.31        30.64        28.04 
TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       26.93        38.30        16.34        68.91        45.96 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             21.14               0.46 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             57.90             150.41 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             21.14              41.19 
[1] "21.1 - 57.9 (21.1)" "0.5 - 150.4 (41.2)"
[1] "hr="     "9200000"
D17V2, continuous
D17V3, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    1  2
  18P GAIN WILD-TYPE 26 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    2
  18P GAIN WILD-TYPE   26   94
                      clus
vv                     18P GAIN MUTATED 18P GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM                1                 26
  THYMUS                              2                 94
[1] 2 2
[1] FALSE
D17V4, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    1  2
  18P GAIN WILD-TYPE 58 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    2
  18P GAIN WILD-TYPE   58   62
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                1                 58
  MALE                  2                 62
[1] 2 2
[1] FALSE
D17V5, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    1  2
  18P GAIN WILD-TYPE 80 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    2
  18P GAIN WILD-TYPE   80   40
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 1                 80
  YES                2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  18P GAIN MUTATED                 0                1                0
  18P GAIN WILD-TYPE              17               37               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  18P GAIN MUTATED                  0                0               2
  18P GAIN WILD-TYPE               30               12               9
D17V6, multiclass
                  clus
vv                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                1                 37
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                0                 30
  THYMOMA; TYPE B3                0                 12
  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
  18P GAIN MUTATED       0                         0     3
  18P GAIN WILD-TYPE    13                         6    99
D17V7, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    1  2
  18P GAIN WILD-TYPE  8 98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    2
  18P GAIN WILD-TYPE    8   98
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO                2                 98
[1] 2 2
[1] FALSE

Clustering(18) Variable = 18Q GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED     3   0
  18Q GAIN WILD-TYPE 110   9
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                119 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                  9 
$`18Q GAIN MUTATED`
TCGA-3S-A8YW TCGA-XU-A936 TCGA-ZB-A96F 
       21.14        21.14        57.90 

$`18Q GAIN 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-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        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-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
       54.08       150.41        64.83        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-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R 
       12.72        84.23        32.25        37.81       112.11        90.05 
TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y 
       45.24       149.98         4.08       107.80        77.03       114.67 
TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW 
      120.43        82.65        52.90        70.65        58.82       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-A962 TCGA-ZB-A963 
       35.18        49.78        23.38         5.92        54.15        48.72 
TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D 
       42.31        12.46        34.39        77.39        72.69        64.44 
TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M 
       59.80        52.80        49.45        54.35        50.27         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
       34.52        24.76        22.19        59.31        30.64        28.04 
TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       26.93        38.30        16.34        68.91        45.96 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             21.14               0.46 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             57.90             150.41 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             21.14              41.19 
[1] "21.1 - 57.9 (21.1)" "0.5 - 150.4 (41.2)"
[1] "hr="     "9200000"
D18V2, continuous
D18V3, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    1  2
  18Q GAIN WILD-TYPE 26 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    2
  18Q GAIN WILD-TYPE   26   94
                      clus
vv                     18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM                1                 26
  THYMUS                              2                 94
[1] 2 2
[1] FALSE
D18V4, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    1  2
  18Q GAIN WILD-TYPE 58 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    2
  18Q GAIN WILD-TYPE   58   62
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                 58
  MALE                  2                 62
[1] 2 2
[1] FALSE
D18V5, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    1  2
  18Q GAIN WILD-TYPE 80 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    2
  18Q GAIN WILD-TYPE   80   40
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 1                 80
  YES                2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  18Q GAIN MUTATED                 0                1                0
  18Q GAIN WILD-TYPE              17               37               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  18Q GAIN MUTATED                  0                0               2
  18Q GAIN WILD-TYPE               30               12               9
D18V6, multiclass
                  clus
vv                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                1                 37
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                0                 30
  THYMOMA; TYPE B3                0                 12
  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
  18Q GAIN MUTATED       0                         0     3
  18Q GAIN WILD-TYPE    13                         6    99
D18V7, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    1  2
  18Q GAIN WILD-TYPE  8 98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    2
  18Q GAIN WILD-TYPE    8   98
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO                2                 98
[1] 2 2
[1] FALSE

Clustering(19) Variable = 19P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED     3   0
  19P GAIN WILD-TYPE 110   9
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                119 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 0                  9 
$`19P GAIN MUTATED`
TCGA-4V-A9QR TCGA-X7-A8M3 TCGA-XU-A930 
       25.64         1.64        82.65 

$`19P GAIN 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-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       51.68        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-A8M4 TCGA-X7-A8M5 
       23.18         9.50        14.50        42.15       125.19        54.08 
TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      150.41        64.83        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-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       84.23        32.25        37.81       112.11        90.05        45.24 
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-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-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46        34.39        77.39        72.69        64.44        59.80 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M 
       57.90        52.80        49.45        54.35        50.27         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
       34.52        24.76        22.19        59.31        30.64        28.04 
TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       26.93        38.30        16.34        68.91        45.96 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              1.64               0.46 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             82.65             150.41 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             25.64              41.19 
[1] "1.6 - 82.7 (25.6)"  "0.5 - 150.4 (41.2)"
[1] "hr="     "9300000"
D19V2, continuous
D19V3, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    0  3
  19P GAIN WILD-TYPE 27 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    3
  19P GAIN WILD-TYPE   27   93
                      clus
vv                     19P GAIN MUTATED 19P GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM                0                 27
  THYMUS                              3                 93
[1] 2 2
[1] FALSE
D19V4, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    2  1
  19P GAIN WILD-TYPE 57 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2    1
  19P GAIN WILD-TYPE   57   63
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                2                 57
  MALE                  1                 63
[1] 2 2
[1] FALSE
D19V5, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    1  2
  19P GAIN WILD-TYPE 80 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    2
  19P GAIN WILD-TYPE   80   40
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 1                 80
  YES                2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  19P GAIN MUTATED                 0                0                0
  19P GAIN WILD-TYPE              17               38               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  19P GAIN MUTATED                  0                3               0
  19P GAIN WILD-TYPE               30                9              11
D19V6, multiclass
                  clus
vv                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                0                 38
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                0                 30
  THYMOMA; TYPE B3                3                  9
  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
  19P GAIN MUTATED       0                         0     3
  19P GAIN WILD-TYPE    13                         6    99
D19V7, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    0  3
  19P GAIN WILD-TYPE  9 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    3
  19P GAIN WILD-TYPE    9   97
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                3                 97
[1] 2 2
[1] FALSE

Clustering(20) Variable = 19Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED     3   0
  19Q GAIN WILD-TYPE 110   9
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                119 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                  9 
$`19Q GAIN MUTATED`
TCGA-4V-A9QR TCGA-X7-A8M3 TCGA-XU-A930 
       25.64         1.64        82.65 

$`19Q GAIN 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-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       51.68        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-A8M4 TCGA-X7-A8M5 
       23.18         9.50        14.50        42.15       125.19        54.08 
TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      150.41        64.83        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-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       84.23        32.25        37.81       112.11        90.05        45.24 
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-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-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46        34.39        77.39        72.69        64.44        59.80 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M 
       57.90        52.80        49.45        54.35        50.27         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
       34.52        24.76        22.19        59.31        30.64        28.04 
TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       26.93        38.30        16.34        68.91        45.96 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              1.64               0.46 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             82.65             150.41 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             25.64              41.19 
[1] "1.6 - 82.7 (25.6)"  "0.5 - 150.4 (41.2)"
[1] "hr="     "9300000"
D20V2, continuous
D20V3, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    0  3
  19Q GAIN WILD-TYPE 27 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0    3
  19Q GAIN WILD-TYPE   27   93
                      clus
vv                     19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM                0                 27
  THYMUS                              3                 93
[1] 2 2
[1] FALSE
D20V4, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    2  1
  19Q GAIN WILD-TYPE 57 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    1
  19Q GAIN WILD-TYPE   57   63
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                2                 57
  MALE                  1                 63
[1] 2 2
[1] FALSE
D20V5, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    1  2
  19Q GAIN WILD-TYPE 80 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1    2
  19Q GAIN WILD-TYPE   80   40
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 1                 80
  YES                2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  19Q GAIN MUTATED                 0                0                0
  19Q GAIN WILD-TYPE              17               38               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  19Q GAIN MUTATED                  0                3               0
  19Q GAIN WILD-TYPE               30                9              11
D20V6, multiclass
                  clus
vv                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                0                 38
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                0                 30
  THYMOMA; TYPE B3                3                  9
  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
  19Q GAIN MUTATED       0                         0     3
  19Q GAIN WILD-TYPE    13                         6    99
D20V7, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    0  3
  19Q GAIN WILD-TYPE  9 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0    3
  19Q GAIN WILD-TYPE    9   97
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                3                 97
[1] 2 2
[1] FALSE

Clustering(21) Variable = 20P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED     9   1
  20P GAIN WILD-TYPE 104   8
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                10                112 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 1                  8 
$`20P GAIN MUTATED`
TCGA-4V-A9QJ TCGA-4V-A9QR TCGA-5U-AB0D TCGA-5U-AB0E TCGA-X7-A8M3 TCGA-XM-A8RC 
       93.67        25.64        23.47        22.59         1.64        97.41 
TCGA-XU-A92X TCGA-XU-A933 TCGA-XU-A936 TCGA-ZC-AAA7 
       77.03        58.82        21.14        28.04 

$`20P GAIN 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-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ 
       34.52        96.53        62.73        41.19        31.89        51.68 
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-5V-A9RR 
       12.89        68.12        49.41        27.45        34.65        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-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 
       42.15       125.19        54.08       150.41        64.83        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF 
       40.11        52.54        48.92        37.61        13.87        26.20 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O 
       11.93        12.72        84.23        32.25        37.81       112.11 
TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92Y 
       90.05        45.24       149.98         4.08       107.80       114.67 
TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-AAXW TCGA-XU-AAXX 
      120.43        82.65        52.90        70.65       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-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46        34.39        77.39        72.69        64.44        59.80 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M 
       57.90        52.80        49.45        54.35        50.27         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAAA 
       34.52        24.76        22.19        59.31        30.64        26.93 
TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       38.30        16.34        68.91        45.96 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              1.64               0.46 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             97.41             150.41 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             26.84              41.67 
[1] "1.6 - 97.4 (26.8)"  "0.5 - 150.4 (41.7)"
[1] "hr=" "1.7"
D21V2, continuous
D21V3, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    4  6
  20P GAIN WILD-TYPE 23 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      4    6
  20P GAIN WILD-TYPE   23   90
                      clus
vv                     20P GAIN MUTATED 20P GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM                4                 23
  THYMUS                              6                 90
[1] 2 2
[1] FALSE
D21V4, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    5  5
  20P GAIN WILD-TYPE 54 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5    5
  20P GAIN WILD-TYPE   54   59
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                5                 54
  MALE                  5                 59
[1] 2 2
[1] FALSE
D21V5, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    5  5
  20P GAIN WILD-TYPE 76 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5    5
  20P GAIN WILD-TYPE   76   37
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 5                 76
  YES                5                 37
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  20P GAIN MUTATED                 0                0                0
  20P GAIN WILD-TYPE              17               38               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  20P GAIN MUTATED                  2                4               4
  20P GAIN WILD-TYPE               28                8               7
D21V6, multiclass
                  clus
vv                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                0                 38
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                2                 28
  THYMOMA; TYPE B3                4                  8
  THYMOMA; TYPE C                 4                  7
[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
  20P GAIN MUTATED       2                         0     8
  20P GAIN WILD-TYPE    11                         6    94
D21V7, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    2                 11
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    8                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    2  8
  20P GAIN WILD-TYPE  7 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2    8
  20P GAIN WILD-TYPE    7   92
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO                8                 92
[1] 2 2
[1] FALSE

Clustering(22) Variable = 20Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED     9   1
  20Q GAIN WILD-TYPE 104   8
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                112 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 1                  8 
$`20Q GAIN MUTATED`
TCGA-4V-A9QJ TCGA-4V-A9QR TCGA-5U-AB0D TCGA-5U-AB0E TCGA-X7-A8M3 TCGA-XM-A8RC 
       93.67        25.64        23.47        22.59         1.64        97.41 
TCGA-XU-A92X TCGA-XU-A933 TCGA-XU-A936 TCGA-ZC-AAA7 
       77.03        58.82        21.14        28.04 

$`20Q GAIN 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-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ 
       34.52        96.53        62.73        41.19        31.89        51.68 
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-5V-A9RR 
       12.89        68.12        49.41        27.45        34.65        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-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 
       42.15       125.19        54.08       150.41        64.83        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF 
       40.11        52.54        48.92        37.61        13.87        26.20 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O 
       11.93        12.72        84.23        32.25        37.81       112.11 
TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92Y 
       90.05        45.24       149.98         4.08       107.80       114.67 
TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-AAXW TCGA-XU-AAXX 
      120.43        82.65        52.90        70.65       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-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46        34.39        77.39        72.69        64.44        59.80 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M 
       57.90        52.80        49.45        54.35        50.27         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAAA 
       34.52        24.76        22.19        59.31        30.64        26.93 
TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       38.30        16.34        68.91        45.96 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              1.64               0.46 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             97.41             150.41 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             26.84              41.67 
[1] "1.6 - 97.4 (26.8)"  "0.5 - 150.4 (41.7)"
[1] "hr=" "1.7"
D22V2, continuous
D22V3, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    4  6
  20Q GAIN WILD-TYPE 23 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4    6
  20Q GAIN WILD-TYPE   23   90
                      clus
vv                     20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM                4                 23
  THYMUS                              6                 90
[1] 2 2
[1] FALSE
D22V4, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    5  5
  20Q GAIN WILD-TYPE 54 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5    5
  20Q GAIN WILD-TYPE   54   59
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                5                 54
  MALE                  5                 59
[1] 2 2
[1] FALSE
D22V5, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    5  5
  20Q GAIN WILD-TYPE 76 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5    5
  20Q GAIN WILD-TYPE   76   37
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 5                 76
  YES                5                 37
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  20Q GAIN MUTATED                 0                0                0
  20Q GAIN WILD-TYPE              17               38               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  20Q GAIN MUTATED                  2                4               4
  20Q GAIN WILD-TYPE               28                8               7
D22V6, multiclass
                  clus
vv                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                0                 38
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                2                 28
  THYMOMA; TYPE B3                4                  8
  THYMOMA; TYPE C                 4                  7
[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
  20Q GAIN MUTATED       2                         0     8
  20Q GAIN WILD-TYPE    11                         6    94
D22V7, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    2                 11
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    8                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    2  8
  20Q GAIN WILD-TYPE  7 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2    8
  20Q GAIN WILD-TYPE    7   92
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO                8                 92
[1] 2 2
[1] FALSE

Clustering(23) Variable = 21Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED     3   0
  21Q GAIN WILD-TYPE 110   9
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                119 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 0                  9 
$`21Q GAIN MUTATED`
TCGA-X7-A8M3 TCGA-XU-A936 TCGA-ZB-A969 
        1.64        21.14        34.39 

$`21Q GAIN 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-A8M4 
       22.85        23.18         9.50        14.50        42.15       125.19 
TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
       54.08       150.41        64.83        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-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R 
       12.72        84.23        32.25        37.81       112.11        90.05 
TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y 
       45.24       149.98         4.08       107.80        77.03       114.67 
TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW 
      120.43        82.65        52.90        70.65        58.82       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-A962 TCGA-ZB-A963 
       35.18        49.78        23.38         5.92        54.15        48.72 
TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       42.31        12.46        77.39        72.69        64.44        59.80 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M 
       57.90        52.80        49.45        54.35        50.27         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
       34.52        24.76        22.19        59.31        30.64        28.04 
TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       26.93        38.30        16.34        68.91        45.96 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              1.64               0.46 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             34.39             150.41 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             21.14              42.15 
[1] "1.6 - 34.4 (21.1)"  "0.5 - 150.4 (42.1)"
[1] "hr="     "9100000"
D23V2, continuous
D23V3, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    2  1
  21Q GAIN WILD-TYPE 25 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2    1
  21Q GAIN WILD-TYPE   25   95
                      clus
vv                     21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM                2                 25
  THYMUS                              1                 95
[1] 2 2
[1] FALSE
D23V4, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    3  0
  21Q GAIN WILD-TYPE 56 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    0
  21Q GAIN WILD-TYPE   56   64
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                3                 56
  MALE                  0                 64
[1] 2 2
[1] FALSE
D23V5, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    2  1
  21Q GAIN WILD-TYPE 79 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2    1
  21Q GAIN WILD-TYPE   79   41
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 2                 79
  YES                1                 41
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  21Q GAIN MUTATED                 0                0                0
  21Q GAIN WILD-TYPE              17               38               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  21Q GAIN MUTATED                  0                1               2
  21Q GAIN WILD-TYPE               30               11               9
D23V6, multiclass
                  clus
vv                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                0                 38
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                0                 30
  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
  21Q GAIN MUTATED       0                         0     3
  21Q GAIN WILD-TYPE    13                         6    99
D23V7, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    0  3
  21Q GAIN WILD-TYPE  9 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0    3
  21Q GAIN WILD-TYPE    9   97
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                3                 97
[1] 2 2
[1] FALSE

Clustering(24) Variable = 22Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED     4   0
  22Q GAIN WILD-TYPE 109   9
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                118 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 0                  9 
$`22Q GAIN MUTATED`
TCGA-4V-A9QR TCGA-4X-A9FD TCGA-X7-A8M3 TCGA-XU-A92X 
       25.64        49.41         1.64        77.03 

$`22Q GAIN 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-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       51.68        25.45        26.73        20.61        20.71        14.27 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D 
       21.99        12.89        68.12        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-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 
        9.50        14.50        42.15       125.19        54.08       150.41 
TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       64.83        83.28        40.11        52.54        48.92        37.61 
TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
       97.41        13.87        26.20        11.93        12.72        84.23 
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-A92Y TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 
        4.08       107.80       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-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F 
       34.39        77.39        72.69        64.44        59.80        57.90 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O 
       52.80        49.45        54.35        50.27         0.46        34.52 
TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       24.76        22.19        59.31        30.64        28.04        26.93 
TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       38.30        16.34        68.91        45.96 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1.64               0.46 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             77.03             150.41 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            37.525             40.650 
[1] "1.6 - 77.0 (37.5)"  "0.5 - 150.4 (40.6)"
[1] "hr="     "9300000"
D24V2, continuous
D24V3, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    0  4
  22Q GAIN WILD-TYPE 27 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    4
  22Q GAIN WILD-TYPE   27   92
                      clus
vv                     22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM                0                 27
  THYMUS                              4                 92
[1] 2 2
[1] FALSE
D24V4, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    3  1
  22Q GAIN WILD-TYPE 56 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3    1
  22Q GAIN WILD-TYPE   56   63
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                3                 56
  MALE                  1                 63
[1] 2 2
[1] FALSE
D24V5, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    3  1
  22Q GAIN WILD-TYPE 78 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3    1
  22Q GAIN WILD-TYPE   78   41
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 3                 78
  YES                1                 41
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  22Q GAIN MUTATED                 0                0                0
  22Q GAIN WILD-TYPE              17               38               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  22Q GAIN MUTATED                  2                2               0
  22Q GAIN WILD-TYPE               28               10              11
D24V6, multiclass
                  clus
vv                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                0                 38
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                2                 28
  THYMOMA; TYPE B3                2                 10
  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
  22Q GAIN MUTATED       1                         0     3
  22Q GAIN WILD-TYPE    12                         6    99
D24V7, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    0  4
  22Q GAIN WILD-TYPE  9 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    4
  22Q GAIN WILD-TYPE    9   96
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                4                 96
[1] 2 2
[1] FALSE

Clustering(25) Variable = XQ GAIN MUTATION ANALYSIS
D25V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED     3   1
  XQ GAIN WILD-TYPE 110   8
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4               118 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                 8 
$`XQ GAIN MUTATED`
TCGA-3G-AB0T TCGA-4V-A9QR TCGA-X7-A8M3 TCGA-ZB-A96F 
       81.80        25.64         1.64        57.90 

$`XQ GAIN 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-AB14 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L 
       59.15        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-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-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 
        9.50        14.50        42.15       125.19        54.08       150.41 
TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       64.83        83.28        40.11        52.54        48.92        37.61 
TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
       97.41        13.87        26.20        11.93        12.72        84.23 
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-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46        34.39        77.39        72.69        64.44        59.80 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O 
       52.80        49.45        54.35        50.27         0.46        34.52 
TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       24.76        22.19        59.31        30.64        28.04        26.93 
TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       38.30        16.34        68.91        45.96 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             1.64              0.46 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            81.80            150.41 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            41.77             40.65 
[1] "1.6 - 81.8 (41.8)"  "0.5 - 150.4 (40.6)"
[1] "hr=" "4.9"
D25V2, continuous
D25V3, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    1  3
  XQ GAIN WILD-TYPE 26 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1    3
  XQ GAIN WILD-TYPE   26   93
                      clus
vv                     XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ANTERIOR MEDIASTINUM               1                26
  THYMUS                             3                93
[1] 2 2
[1] FALSE
D25V4, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    2  2
  XQ GAIN WILD-TYPE 57 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2    2
  XQ GAIN WILD-TYPE   57   62
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               2                57
  MALE                 2                62
[1] 2 2
[1] FALSE
D25V5, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    2  2
  XQ GAIN WILD-TYPE 79 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2    2
  XQ GAIN WILD-TYPE   79   40
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                2                79
  YES               2                40
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  XQ GAIN MUTATED                 0                1                1
  XQ GAIN WILD-TYPE              17               37               14
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  XQ GAIN MUTATED                  0                2               0
  XQ GAIN WILD-TYPE               30               10              11
D25V6, multiclass
                  clus
vv                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               1                37
  THYMOMA; TYPE B1               1                14
  THYMOMA; TYPE B2               0                30
  THYMOMA; TYPE B3               2                10
  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
  XQ GAIN MUTATED       0                         0     4
  XQ GAIN WILD-TYPE    13                         6    98
D25V7, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   4                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"
D25V8, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    0  4
  XQ GAIN WILD-TYPE  9 96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    4
  XQ GAIN WILD-TYPE    9   96
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               4                96
[1] 2 2
[1] FALSE

Clustering(26) Variable = 1P LOSS MUTATION ANALYSIS
D26V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED     5   0
  1P LOSS WILD-TYPE 108   9
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5               117 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                0                 9 
$`1P LOSS MUTATED`
TCGA-3S-A8YW TCGA-4V-A9QN TCGA-4X-A9FD TCGA-XU-A930 TCGA-XU-A936 
       21.14        31.89        49.41        82.65        21.14 

$`1P LOSS 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-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        18.77        34.52 
TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QR 
       96.53        93.67        62.73        41.19        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-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E 
       12.89        68.12        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-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       64.83        83.28        40.11        52.54        48.92        37.61 
TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
       97.41        13.87        26.20        11.93        12.72        84.23 
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-A931 
        4.08       107.80        77.03       114.67       120.43        52.90 
TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ 
       70.65        58.82       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-A96P 
       49.45        54.35        50.27         0.46        34.52        24.76 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
       22.19        59.31        30.64        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       16.34        68.91        45.96 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            21.14              0.46 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            82.65            150.41 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            31.89             41.19 
[1] "21.1 - 82.7 (31.9)" "0.5 - 150.4 (41.2)"
[1] "hr="     "2.6e+07"
D26V2, continuous
D26V3, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  4
  1P LOSS WILD-TYPE 26 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    4
  1P LOSS WILD-TYPE   26   92
                      clus
vv                     1P LOSS MUTATED 1P LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM               1                26
  THYMUS                             4                92
[1] 2 2
[1] FALSE
D26V4, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    3  2
  1P LOSS WILD-TYPE 56 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    2
  1P LOSS WILD-TYPE   56   62
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               3                56
  MALE                 2                62
[1] 2 2
[1] FALSE
D26V5, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  4
  1P LOSS WILD-TYPE 80 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    4
  1P LOSS WILD-TYPE   80   38
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                1                80
  YES               4                38
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  1P LOSS MUTATED                 0                0                0
  1P LOSS WILD-TYPE              17               38               15
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  1P LOSS MUTATED                  1                2               2
  1P LOSS WILD-TYPE               29               10               9
D26V6, multiclass
                  clus
vv                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               0                38
  THYMOMA; TYPE B1               0                15
  THYMOMA; TYPE B2               1                29
  THYMOMA; TYPE B3               2                10
  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
  1P LOSS MUTATED       0                         0     5
  1P LOSS WILD-TYPE    13                         6    97
D26V7, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   5                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"
D26V8, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    2  3
  1P LOSS WILD-TYPE  7 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2    3
  1P LOSS WILD-TYPE    7   97
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO               3                97
[1] 2 2
[1] FALSE

Clustering(27) Variable = 3P LOSS MUTATION ANALYSIS
D27V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    10   2
  3P LOSS WILD-TYPE 103   7
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               12               110 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                 7 
$`3P LOSS MUTATED`
TCGA-3G-AB14 TCGA-3S-A8YW TCGA-4V-A9QN TCGA-4X-A9FD TCGA-5U-AB0E TCGA-XM-A8RC 
       25.48        21.14        31.89        49.41        22.59        97.41 
TCGA-XU-A92X TCGA-XU-A930 TCGA-YT-A95G TCGA-ZB-A966 TCGA-ZB-A96I TCGA-ZC-AAAA 
       77.03        82.65        49.78        12.46        54.35        26.93 

$`3P LOSS 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-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS 
       93.67        62.73        41.19        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-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5V-A9RR TCGA-X7-A8D6 
       68.12        27.45        34.65        23.47        27.19       138.90 
TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE 
       10.68         1.91        65.49        59.11        36.62        32.25 
TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 
       29.62        22.85        23.18         9.50        14.50        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 
        1.64       125.19        54.08       150.41        64.83        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF 
       40.11        52.54        48.92        37.61        13.87        26.20 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O 
       11.93        12.72        84.23        32.25        37.81       112.11 
TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92Y 
       90.05        45.24       149.98         4.08       107.80       114.67 
TCGA-XU-A92Z TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXW 
      120.43        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-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       35.18        23.38         5.92        54.15        48.72        42.31 
TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F 
       34.39        77.39        72.69        64.44        59.80        57.90 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
       52.80        49.45        50.27         0.46        34.52        24.76 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH 
       22.19        59.31        30.64        28.04        38.30        16.34 
TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       68.91        45.96 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            12.46              0.46 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            97.41            150.41 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            40.65             40.65 
[1] "12.5 - 97.4 (40.6)" "0.5 - 150.4 (40.6)"
[1] "hr=" "3.1"
D27V2, continuous
D27V3, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    4  8
  3P LOSS WILD-TYPE 23 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4    8
  3P LOSS WILD-TYPE   23   88
                      clus
vv                     3P LOSS MUTATED 3P LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM               4                23
  THYMUS                             8                88
[1] 2 2
[1] FALSE
D27V4, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    5  7
  3P LOSS WILD-TYPE 54 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5    7
  3P LOSS WILD-TYPE   54   57
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               5                54
  MALE                 7                57
[1] 2 2
[1] FALSE
D27V5, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    6  6
  3P LOSS WILD-TYPE 75 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      6    6
  3P LOSS WILD-TYPE   75   36
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                6                75
  YES               6                36
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  3P LOSS MUTATED                 0                1                0
  3P LOSS WILD-TYPE              17               37               15
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  3P LOSS MUTATED                  6                3               2
  3P LOSS WILD-TYPE               24                9               9
D27V6, multiclass
                  clus
vv                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               1                37
  THYMOMA; TYPE B1               0                15
  THYMOMA; TYPE B2               6                24
  THYMOMA; TYPE B3               3                 9
  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
  3P LOSS MUTATED       1                         0    11
  3P LOSS WILD-TYPE    12                         6    91
D27V7, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  11                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    4  7
  3P LOSS WILD-TYPE  5 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4    7
  3P LOSS WILD-TYPE    5   93
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO               7                93
[1] 2 2
[1] FALSE

Clustering(28) Variable = 3Q LOSS MUTATION ANALYSIS
D28V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     7   0
  3Q LOSS WILD-TYPE 106   9
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                7               115 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                0                 9 
$`3Q LOSS MUTATED`
TCGA-3S-A8YW TCGA-5U-AB0E TCGA-XM-A8RC TCGA-XU-A92X TCGA-XU-A930 TCGA-YT-A95G 
       21.14        22.59        97.41        77.03        82.65        49.78 
TCGA-ZC-AAAA 
       26.93 

$`3Q LOSS 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-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        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-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB 
       23.47        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-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 
        9.50        14.50        42.15         1.64       125.19        54.08 
TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      150.41        64.83        83.28        40.11        52.54        48.92 
TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
       37.61        13.87        26.20        11.93        12.72        84.23 
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-A92Y TCGA-XU-A92Z TCGA-XU-A931 TCGA-XU-A932 
        4.08       107.80       114.67       120.43        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-A95H TCGA-ZB-A961 
       49.38       107.44        24.66        35.18        23.38         5.92 
TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A 
       54.15        48.72        42.31        12.46        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-A96P TCGA-ZB-A96Q 
       54.35        50.27         0.46        34.52        24.76        22.19 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       59.31        30.64        28.04        38.30        16.34        68.91 
TCGA-ZT-A8OM 
       45.96 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            21.14              0.46 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            97.41            150.41 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            49.78             40.11 
[1] "21.1 - 97.4 (49.8)" "0.5 - 150.4 (40.1)"
[1] "hr="     "7.4e+07"
D28V2, continuous
D28V3, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    3  4
  3Q LOSS WILD-TYPE 24 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    4
  3Q LOSS WILD-TYPE   24   92
                      clus
vv                     3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM               3                24
  THYMUS                             4                92
[1] 2 2
[1] FALSE
D28V4, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    1  6
  3Q LOSS WILD-TYPE 58 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    6
  3Q LOSS WILD-TYPE   58   58
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               1                58
  MALE                 6                58
[1] 2 2
[1] FALSE
D28V5, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    3  4
  3Q LOSS WILD-TYPE 78 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    4
  3Q LOSS WILD-TYPE   78   38
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                3                78
  YES               4                38
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  3Q LOSS MUTATED                 0                0                0
  3Q LOSS WILD-TYPE              17               38               15
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  3Q LOSS MUTATED                  4                2               1
  3Q LOSS WILD-TYPE               26               10              10
D28V6, multiclass
                  clus
vv                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               0                38
  THYMOMA; TYPE B1               0                15
  THYMOMA; TYPE B2               4                26
  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
  3Q LOSS MUTATED       1                         0     6
  3Q LOSS WILD-TYPE    12                         6    96
D28V7, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   6                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    3  3
  3Q LOSS WILD-TYPE  6 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    3
  3Q LOSS WILD-TYPE    6   97
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 6
  NOT HISPANIC OR LATINO               3                97
[1] 2 2
[1] FALSE

Clustering(29) Variable = 4P LOSS MUTATION ANALYSIS
D29V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED     5   0
  4P LOSS WILD-TYPE 108   9
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                5               117 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                0                 9 
$`4P LOSS MUTATED`
TCGA-4V-A9QJ TCGA-4X-A9FD TCGA-XM-A8RC TCGA-XU-A930 TCGA-YT-A95G 
       93.67        49.41        97.41        82.65        49.78 

$`4P LOSS 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-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ 
       34.52        96.53        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-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D 
       21.99        12.89        68.12        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-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 
        9.50        14.50        42.15         1.64       125.19        54.08 
TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      150.41        64.83        83.28        40.11        52.54        48.92 
TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
       37.61        13.87        26.20        11.93        12.72        84.23 
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-A931 
        4.08       107.80        77.03       114.67       120.43        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-A95H 
       50.53        49.38       107.44        24.66        35.18        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-A96P 
       49.45        54.35        50.27         0.46        34.52        24.76 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
       22.19        59.31        30.64        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       16.34        68.91        45.96 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            49.41              0.46 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            97.41            150.41 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            82.65             37.81 
[1] "49.4 - 97.4 (82.7)" "0.5 - 150.4 (37.8)"
[1] "hr="     "7.6e+07"
D29V2, continuous
D29V3, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    1  4
  4P LOSS WILD-TYPE 26 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1    4
  4P LOSS WILD-TYPE   26   92
                      clus
vv                     4P LOSS MUTATED 4P LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM               1                26
  THYMUS                             4                92
[1] 2 2
[1] FALSE
D29V4, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    2  3
  4P LOSS WILD-TYPE 57 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      2    3
  4P LOSS WILD-TYPE   57   61
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               2                57
  MALE                 3                61
[1] 2 2
[1] FALSE
D29V5, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    3  2
  4P LOSS WILD-TYPE 78 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3    2
  4P LOSS WILD-TYPE   78   40
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                3                78
  YES               2                40
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  4P LOSS MUTATED                 0                0                0
  4P LOSS WILD-TYPE              17               38               15
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  4P LOSS MUTATED                  3                2               0
  4P LOSS WILD-TYPE               27               10              11
D29V6, multiclass
                  clus
vv                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               0                38
  THYMOMA; TYPE B1               0                15
  THYMOMA; TYPE B2               3                27
  THYMOMA; TYPE B3               2                10
  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
  4P LOSS MUTATED       0                         0     5
  4P LOSS WILD-TYPE    13                         6    97
D29V7, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   5                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"
D29V8, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    0  4
  4P LOSS WILD-TYPE  9 96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      0    4
  4P LOSS WILD-TYPE    9   96
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               4                96
[1] 2 2
[1] FALSE

Clustering(30) Variable = 4Q LOSS MUTATION ANALYSIS
D30V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED     4   0
  4Q LOSS WILD-TYPE 109   9
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4               118 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                0                 9 
$`4Q LOSS MUTATED`
TCGA-4V-A9QJ TCGA-XM-A8RC TCGA-XU-A930 TCGA-YT-A95G 
       93.67        97.41        82.65        49.78 

$`4Q LOSS 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-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ 
       34.52        96.53        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-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
       54.08       150.41        64.83        83.28        40.11        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI 
       48.92        37.61        13.87        26.20        11.93        12.72 
TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       84.23        32.25        37.81       112.11        90.05        45.24 
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-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-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-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F 
       34.39        77.39        72.69        64.44        59.80        57.90 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O 
       52.80        49.45        54.35        50.27         0.46        34.52 
TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       24.76        22.19        59.31        30.64        28.04        26.93 
TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       38.30        16.34        68.91        45.96 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            49.78              0.46 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            97.41            150.41 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           88.160            38.055 
[1] "49.8 - 97.4 (88.2)" "0.5 - 150.4 (38.1)"
[1] "hr="     "2.8e+07"
D30V2, continuous
D30V3, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    1  3
  4Q LOSS WILD-TYPE 26 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    3
  4Q LOSS WILD-TYPE   26   93
                      clus
vv                     4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM               1                26
  THYMUS                             3                93
[1] 2 2
[1] FALSE
D30V4, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    1  3
  4Q LOSS WILD-TYPE 58 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    3
  4Q LOSS WILD-TYPE   58   61
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               1                58
  MALE                 3                61
[1] 2 2
[1] FALSE
D30V5, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    2  2
  4Q LOSS WILD-TYPE 79 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2    2
  4Q LOSS WILD-TYPE   79   40
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                2                79
  YES               2                40
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  4Q LOSS MUTATED                 0                0                0
  4Q LOSS WILD-TYPE              17               38               15
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  4Q LOSS MUTATED                  2                2               0
  4Q LOSS WILD-TYPE               28               10              11
D30V6, multiclass
                  clus
vv                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               0                38
  THYMOMA; TYPE B1               0                15
  THYMOMA; TYPE B2               2                28
  THYMOMA; TYPE B3               2                10
  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
  4Q LOSS MUTATED       0                         0     4
  4Q LOSS WILD-TYPE    13                         6    98
D30V7, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   4                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"
D30V8, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    0  3
  4Q LOSS WILD-TYPE  9 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      0    3
  4Q LOSS WILD-TYPE    9   97
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               3                97
[1] 2 2
[1] FALSE

Clustering(31) Variable = 6P LOSS MUTATION ANALYSIS
D31V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   17  4
  6P LOSS WILD-TYPE 96  5
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               21               101 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                4                 5 
$`6P LOSS MUTATED`
TCGA-XM-A8RD TCGA-3G-AB14 TCGA-3S-A8YW TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4V-A9QW 
       50.83        25.48        21.14        31.89        25.64        20.71 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-5U-AB0E TCGA-XM-A8RC TCGA-XU-A92X 
       49.41        27.45        23.47        22.59        97.41        77.03 
TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A936 TCGA-YT-A95G TCGA-ZB-A961 
       82.65        52.90        70.65        21.14        49.78         5.92 
TCGA-ZB-A96F TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       57.90        28.04        26.93 

$`6P LOSS WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RG TCGA-XM-AAZ1 TCGA-XU-A92Q 
       95.67        23.57        15.09        12.69        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-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ 
       81.80        15.35        18.77        34.52        96.53        93.67 
TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       62.73        41.19        51.68        25.45        26.73        20.61 
TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-5K-AAAP TCGA-5V-A9RR 
       14.27        21.99        12.89        68.12        34.65        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-A8M7 
       42.15         1.64       125.19        54.08       150.41        64.83 
TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE 
       83.28        40.11        52.54        48.92        37.61        13.87 
TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       26.20        11.93        12.72        84.23        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-A92Y TCGA-XU-A92Z TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY 
      114.67       120.43        58.82       123.68        89.46        62.17 
TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95H 
       50.53        49.38       107.44        24.66        35.18        23.38 
TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A 
       54.15        48.72        42.31        12.46        34.39        77.39 
TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I 
       72.69        64.44        59.80        52.80        49.45        54.35 
TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
       50.27         0.46        34.52        24.76        22.19        59.31 
TCGA-ZB-A96V TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       30.64        38.30        16.34        68.91        45.96 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             5.92              0.46 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            97.41            150.41 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            28.04             42.15 
[1] "5.9 - 97.4 (28.0)"  "0.5 - 150.4 (42.1)"
[1] "hr=" "6.1"
D31V2, continuous
D31V3, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    5 16
  6P LOSS WILD-TYPE 22 80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   16
  6P LOSS WILD-TYPE   22   80
                      clus
vv                     6P LOSS MUTATED 6P LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM               5                22
  THYMUS                            16                80
[1] 2 2
[1] FALSE
D31V4, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    9 12
  6P LOSS WILD-TYPE 50 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      9   12
  6P LOSS WILD-TYPE   50   52
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               9                50
  MALE                12                52
[1] 2 2
[1] FALSE
D31V5, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   12  9
  6P LOSS WILD-TYPE 69 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     12    9
  6P LOSS WILD-TYPE   69   33
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               12                69
  YES               9                33
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  6P LOSS MUTATED                 1                2                0
  6P LOSS WILD-TYPE              16               36               15
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  6P LOSS MUTATED                  8                5               5
  6P LOSS WILD-TYPE               22                7               6
D31V6, multiclass
                  clus
vv                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  THYMOMA; TYPE A                1                16
  THYMOMA; TYPE AB               2                36
  THYMOMA; TYPE B1               0                15
  THYMOMA; TYPE B2               8                22
  THYMOMA; TYPE B3               5                 7
  THYMOMA; TYPE C                5                 6
[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
  6P LOSS MUTATED       2                         0    19
  6P LOSS WILD-TYPE    11                         6    83
D31V7, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   2                11
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  19                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    5 14
  6P LOSS WILD-TYPE  4 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   14
  6P LOSS WILD-TYPE    4   86
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 4
  NOT HISPANIC OR LATINO              14                86
[1] 2 2
[1] FALSE

Clustering(32) Variable = 6Q LOSS MUTATION ANALYSIS
D32V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   17  3
  6Q LOSS WILD-TYPE 96  6
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               20               102 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                3                 6 
$`6Q LOSS MUTATED`
TCGA-XM-A8RD TCGA-3G-AB14 TCGA-3S-A8YW TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4V-A9QW 
       50.83        25.48        21.14        31.89        25.64        20.71 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-5U-AB0E TCGA-X7-A8M0 TCGA-XM-A8RC 
       49.41        27.45        23.47        22.59        14.50        97.41 
TCGA-XU-A92X TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A936 TCGA-YT-A95G TCGA-ZB-A96F 
       77.03        82.65        52.90        21.14        49.78        57.90 
TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       28.04        26.93 

$`6Q LOSS WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RG TCGA-XM-AAZ1 TCGA-XU-A92Q 
       95.67        23.57        15.09        12.69        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-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ 
       81.80        15.35        18.77        34.52        96.53        93.67 
TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       62.73        41.19        51.68        25.45        26.73        20.61 
TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-5K-AAAP TCGA-5V-A9RR 
       14.27        21.99        12.89        68.12        34.65        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-A8M1 
       32.25        29.62        22.85        23.18         9.50        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 
        1.64       125.19        54.08       150.41        64.83        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF 
       40.11        52.54        48.92        37.61        13.87        26.20 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O 
       11.93        12.72        84.23        32.25        37.81       112.11 
TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92Y 
       90.05        45.24       149.98         4.08       107.80       114.67 
TCGA-XU-A92Z TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY 
      120.43        70.65        58.82       123.68        89.46        62.17 
TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95H 
       50.53        49.38       107.44        24.66        35.18        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-A96G TCGA-ZB-A96H 
       77.39        72.69        64.44        59.80        52.80        49.45 
TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       54.35        50.27         0.46        34.52        24.76        22.19 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       59.31        30.64        38.30        16.34        68.91        45.96 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            14.50              0.46 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            97.41            150.41 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           27.745            42.230 
[1] "14.5 - 97.4 (27.7)" "0.5 - 150.4 (42.2)"
[1] "hr=" "3.9"
D32V2, continuous
D32V3, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    5 15
  6Q LOSS WILD-TYPE 22 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      5   15
  6Q LOSS WILD-TYPE   22   81
                      clus
vv                     6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM               5                22
  THYMUS                            15                81
[1] 2 2
[1] FALSE
D32V4, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   10 10
  6Q LOSS WILD-TYPE 49 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     10   10
  6Q LOSS WILD-TYPE   49   54
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              10                49
  MALE                10                54
[1] 2 2
[1] FALSE
D32V5, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   12  8
  6Q LOSS WILD-TYPE 69 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     12    8
  6Q LOSS WILD-TYPE   69   34
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               12                69
  YES               8                34
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  6Q LOSS MUTATED                 0                2                0
  6Q LOSS WILD-TYPE              17               36               15
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  6Q LOSS MUTATED                  8                5               5
  6Q LOSS WILD-TYPE               22                7               6
D32V6, multiclass
                  clus
vv                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               2                36
  THYMOMA; TYPE B1               0                15
  THYMOMA; TYPE B2               8                22
  THYMOMA; TYPE B3               5                 7
  THYMOMA; TYPE C                5                 6
[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
  6Q LOSS MUTATED       1                         0    19
  6Q LOSS WILD-TYPE    12                         6    83
D32V7, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  19                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    5 13
  6Q LOSS WILD-TYPE  4 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      5   13
  6Q LOSS WILD-TYPE    4   87
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 4
  NOT HISPANIC OR LATINO              13                87
[1] 2 2
[1] FALSE

Clustering(33) Variable = 9P LOSS MUTATION ANALYSIS
D33V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED     4   0
  9P LOSS WILD-TYPE 109   9
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                4               118 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                0                 9 
$`9P LOSS MUTATED`
TCGA-3S-A8YW TCGA-XU-A936 TCGA-ZB-A969 TCGA-ZB-A96L 
       21.14        21.14        34.39        50.27 

$`9P LOSS 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-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        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-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
       54.08       150.41        64.83        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-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R 
       12.72        84.23        32.25        37.81       112.11        90.05 
TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y 
       45.24       149.98         4.08       107.80        77.03       114.67 
TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW 
      120.43        82.65        52.90        70.65        58.82       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-A962 TCGA-ZB-A963 
       35.18        49.78        23.38         5.92        54.15        48.72 
TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       42.31        12.46        77.39        72.69        64.44        59.80 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96M TCGA-ZB-A96O 
       57.90        52.80        49.45        54.35         0.46        34.52 
TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       24.76        22.19        59.31        30.64        28.04        26.93 
TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       38.30        16.34        68.91        45.96 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            21.14              0.46 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            50.27            150.41 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           27.765            41.670 
[1] "21.1 - 50.3 (27.8)" "0.5 - 150.4 (41.7)"
[1] "hr="     "9300000"
D33V2, continuous
D33V3, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    2  2
  9P LOSS WILD-TYPE 25 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2    2
  9P LOSS WILD-TYPE   25   94
                      clus
vv                     9P LOSS MUTATED 9P LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM               2                25
  THYMUS                             2                94
[1] 2 2
[1] FALSE
D33V4, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    3  1
  9P LOSS WILD-TYPE 56 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      3    1
  9P LOSS WILD-TYPE   56   63
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               3                56
  MALE                 1                63
[1] 2 2
[1] FALSE
D33V5, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    2  2
  9P LOSS WILD-TYPE 79 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2    2
  9P LOSS WILD-TYPE   79   40
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                2                79
  YES               2                40
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  9P LOSS MUTATED                 0                0                0
  9P LOSS WILD-TYPE              17               38               15
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  9P LOSS MUTATED                  0                1               3
  9P LOSS WILD-TYPE               30               11               8
D33V6, multiclass
                  clus
vv                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               0                38
  THYMOMA; TYPE B1               0                15
  THYMOMA; TYPE B2               0                30
  THYMOMA; TYPE B3               1                11
  THYMOMA; TYPE C                3                 8
[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
  9P LOSS MUTATED       0                         0     4
  9P LOSS WILD-TYPE    13                         6    98
D33V7, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   4                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"
D33V8, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    1  3
  9P LOSS WILD-TYPE  8 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1    3
  9P LOSS WILD-TYPE    8   97
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO               3                97
[1] 2 2
[1] FALSE

Clustering(34) Variable = 10P LOSS MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED     3   0
  10P LOSS WILD-TYPE 110   9
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 3                119 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 0                  9 
$`10P LOSS MUTATED`
TCGA-XM-A8RG TCGA-5U-AB0D TCGA-X7-A8M0 
       12.69        23.47        14.50 

$`10P LOSS 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-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-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-A8DJ TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 
        9.50        42.15         1.64       125.19        54.08       150.41 
TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       64.83        83.28        40.11        52.54        48.92        37.61 
TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
       97.41        13.87        26.20        11.93        12.72        84.23 
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-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46        34.39        77.39        72.69        64.44        59.80 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M 
       57.90        52.80        49.45        54.35        50.27         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
       34.52        24.76        22.19        59.31        30.64        28.04 
TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       26.93        38.30        16.34        68.91        45.96 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             12.69               0.46 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             23.47             150.41 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             14.50              42.15 
[1] "12.7 - 23.5 (14.5)" "0.5 - 150.4 (42.1)"
[1] "hr="     "9300000"
D34V2, continuous
D34V3, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    1  2
  10P LOSS WILD-TYPE 26 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1    2
  10P LOSS WILD-TYPE   26   94
                      clus
vv                     10P LOSS MUTATED 10P LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM                1                 26
  THYMUS                              2                 94
[1] 2 2
[1] FALSE
D34V4, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    2  1
  10P LOSS WILD-TYPE 57 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2    1
  10P LOSS WILD-TYPE   57   63
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                2                 57
  MALE                  1                 63
[1] 2 2
[1] FALSE
D34V5, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    3  0
  10P LOSS WILD-TYPE 78 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      3    0
  10P LOSS WILD-TYPE   78   42
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 3                 78
  YES                0                 42
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  10P LOSS MUTATED                 1                0                0
  10P LOSS WILD-TYPE              16               38               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  10P LOSS MUTATED                  1                0               1
  10P LOSS WILD-TYPE               29               12              10
D34V6, multiclass
                  clus
vv                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  THYMOMA; TYPE A                 1                 16
  THYMOMA; TYPE AB                0                 38
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                1                 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
  10P LOSS MUTATED       0                         0     3
  10P LOSS WILD-TYPE    13                         6    99
D34V7, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    1  2
  10P LOSS WILD-TYPE  8 98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1    2
  10P LOSS WILD-TYPE    8   98
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO                2                 98
[1] 2 2
[1] FALSE

Clustering(35) Variable = 11P LOSS MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED     9   0
  11P LOSS WILD-TYPE 104   9
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 9                113 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 0                  9 
$`11P LOSS MUTATED`
TCGA-4V-A9QN TCGA-4X-A9FD TCGA-5U-AB0D TCGA-5U-AB0E TCGA-XM-A8RC TCGA-XU-A92X 
       31.89        49.41        23.47        22.59        97.41        77.03 
TCGA-XU-A930 TCGA-ZB-A96I TCGA-ZC-AAAA 
       82.65        54.35        26.93 

$`11P LOSS 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-A9QQ 
       34.52        96.53        93.67        62.73        41.19        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-5G-A9ZZ TCGA-5K-AAAP TCGA-5V-A9RR 
       21.99        12.89        68.12        27.45        34.65        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-A8M7 
       42.15         1.64       125.19        54.08       150.41        64.83 
TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE 
       83.28        40.11        52.54        48.92        37.61        13.87 
TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       26.20        11.93        12.72        84.23        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-A92Y TCGA-XU-A92Z TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-A936 
      114.67       120.43        52.90        70.65        58.82        21.14 
TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 
      123.68        89.46        62.17        50.53        49.38       107.44 
TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 
       24.66        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-A96L 
       64.44        59.80        57.90        52.80        49.45        50.27 
TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V 
        0.46        34.52        24.76        22.19        59.31        30.64 
TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       28.04        38.30        16.34        68.91        45.96 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             22.59               0.46 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             97.41             150.41 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             49.41              40.11 
[1] "22.6 - 97.4 (49.4)" "0.5 - 150.4 (40.1)"
[1] "hr="     "7.5e+07"
D35V2, continuous
D35V3, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    5  4
  11P LOSS WILD-TYPE 22 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5    4
  11P LOSS WILD-TYPE   22   92
                      clus
vv                     11P LOSS MUTATED 11P LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM                5                 22
  THYMUS                              4                 92
[1] 2 2
[1] FALSE
D35V4, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    4  5
  11P LOSS WILD-TYPE 55 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4    5
  11P LOSS WILD-TYPE   55   59
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                4                 55
  MALE                  5                 59
[1] 2 2
[1] FALSE
D35V5, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    5  4
  11P LOSS WILD-TYPE 76 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5    4
  11P LOSS WILD-TYPE   76   38
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 5                 76
  YES                4                 38
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  11P LOSS MUTATED                 0                1                0
  11P LOSS WILD-TYPE              17               37               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  11P LOSS MUTATED                  4                3               1
  11P LOSS WILD-TYPE               26                9              10
D35V6, multiclass
                  clus
vv                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                1                 37
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                4                 26
  THYMOMA; TYPE B3                3                  9
  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
  11P LOSS MUTATED       1                         0     8
  11P LOSS WILD-TYPE    12                         6    94
D35V7, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    8                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    4  5
  11P LOSS WILD-TYPE  5 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4    5
  11P LOSS WILD-TYPE    5   95
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO                5                 95
[1] 2 2
[1] FALSE

Clustering(36) Variable = 11Q LOSS MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED     7   0
  11Q LOSS WILD-TYPE 106   9
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                115 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 0                  9 
$`11Q LOSS MUTATED`
TCGA-4V-A9QN TCGA-4X-A9FD TCGA-5U-AB0E TCGA-XM-A8RC TCGA-XU-A92X TCGA-XU-A930 
       31.89        49.41        22.59        97.41        77.03        82.65 
TCGA-ZC-AAAA 
       26.93 

$`11Q LOSS 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-A9QQ 
       34.52        96.53        93.67        62.73        41.19        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-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D 
       21.99        12.89        68.12        27.45        34.65        23.47 
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-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       64.83        83.28        40.11        52.54        48.92        37.61 
TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 
       13.87        26.20        11.93        12.72        84.23        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
       37.81       112.11        90.05        45.24       149.98         4.08 
TCGA-XU-A92W TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 
      107.80       114.67       120.43        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-A95D TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 
      107.44        24.66        35.18        49.78        23.38         5.92 
TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A 
       54.15        48.72        42.31        12.46        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-A96P TCGA-ZB-A96Q 
       54.35        50.27         0.46        34.52        24.76        22.19 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       59.31        30.64        28.04        38.30        16.34        68.91 
TCGA-ZT-A8OM 
       45.96 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             22.59               0.46 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             97.41             150.41 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             49.41              40.11 
[1] "22.6 - 97.4 (49.4)" "0.5 - 150.4 (40.1)"
[1] "hr="     "7.4e+07"
D36V2, continuous
D36V3, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    3  4
  11Q LOSS WILD-TYPE 24 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3    4
  11Q LOSS WILD-TYPE   24   92
                      clus
vv                     11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM                3                 24
  THYMUS                              4                 92
[1] 2 2
[1] FALSE
D36V4, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    2  5
  11Q LOSS WILD-TYPE 57 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2    5
  11Q LOSS WILD-TYPE   57   59
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                2                 57
  MALE                  5                 59
[1] 2 2
[1] FALSE
D36V5, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    3  4
  11Q LOSS WILD-TYPE 78 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3    4
  11Q LOSS WILD-TYPE   78   38
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 3                 78
  YES                4                 38
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  11Q LOSS MUTATED                 0                0                0
  11Q LOSS WILD-TYPE              17               38               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  11Q LOSS MUTATED                  4                3               0
  11Q LOSS WILD-TYPE               26                9              11
D36V6, multiclass
                  clus
vv                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                0                 38
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                4                 26
  THYMOMA; TYPE B3                3                  9
  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
  11Q LOSS MUTATED       1                         0     6
  11Q LOSS WILD-TYPE    12                         6    96
D36V7, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    6                 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"
D36V8, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    3  4
  11Q LOSS WILD-TYPE  6 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3    4
  11Q LOSS WILD-TYPE    6   96
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO                4                 96
[1] 2 2
[1] FALSE

Clustering(37) Variable = 12P LOSS MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED     7   1
  12P LOSS WILD-TYPE 106   8
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 8                114 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                  8 
$`12P LOSS MUTATED`
TCGA-4V-A9QQ TCGA-4X-A9FD TCGA-5U-AB0E TCGA-XU-A92X TCGA-XU-A930 TCGA-ZB-A961 
       51.68        49.41        22.59        77.03        82.65         5.92 
TCGA-ZB-A96F TCGA-ZC-AAAA 
       57.90        26.93 

$`12P LOSS 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-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-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D 
       21.99        12.89        68.12        27.45        34.65        23.47 
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-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       64.83        83.28        40.11        52.54        48.92        37.61 
TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
       97.41        13.87        26.20        11.93        12.72        84.23 
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-A92Y TCGA-XU-A92Z TCGA-XU-A931 TCGA-XU-A932 
        4.08       107.80       114.67       120.43        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-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A 
       54.15        48.72        42.31        12.46        34.39        77.39 
TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I 
       72.69        64.44        59.80        52.80        49.45        54.35 
TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
       50.27         0.46        34.52        24.76        22.19        59.31 
TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       30.64        28.04        38.30        16.34        68.91        45.96 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              5.92               0.46 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             82.65             150.41 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            50.545             39.205 
[1] "5.9 - 82.7 (50.5)"  "0.5 - 150.4 (39.2)"
[1] "hr=" "2.4"
D37V2, continuous
D37V3, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    2  6
  12P LOSS WILD-TYPE 25 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2    6
  12P LOSS WILD-TYPE   25   90
                      clus
vv                     12P LOSS MUTATED 12P LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM                2                 25
  THYMUS                              6                 90
[1] 2 2
[1] FALSE
D37V4, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    2  6
  12P LOSS WILD-TYPE 57 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2    6
  12P LOSS WILD-TYPE   57   58
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                2                 57
  MALE                  6                 58
[1] 2 2
[1] FALSE
D37V5, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    4  4
  12P LOSS WILD-TYPE 77 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      4    4
  12P LOSS WILD-TYPE   77   38
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 4                 77
  YES                4                 38
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  12P LOSS MUTATED                 1                1                0
  12P LOSS WILD-TYPE              16               37               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  12P LOSS MUTATED                  3                3               0
  12P LOSS WILD-TYPE               27                9              11
D37V6, multiclass
                  clus
vv                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  THYMOMA; TYPE A                 1                 16
  THYMOMA; TYPE AB                1                 37
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                3                 27
  THYMOMA; TYPE B3                3                  9
  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
  12P LOSS MUTATED       1                         0     7
  12P LOSS WILD-TYPE    12                         6    95
D37V7, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    7                 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"
D37V8, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    2  6
  12P LOSS WILD-TYPE  7 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2    6
  12P LOSS WILD-TYPE    7   94
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO                6                 94
[1] 2 2
[1] FALSE

Clustering(38) Variable = 12Q LOSS MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED     6   1
  12Q LOSS WILD-TYPE 107   8
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 7                115 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                  8 
$`12Q LOSS MUTATED`
TCGA-4X-A9FD TCGA-5U-AB0E TCGA-XU-A92X TCGA-XU-A930 TCGA-ZB-A961 TCGA-ZB-A96F 
       49.41        22.59        77.03        82.65         5.92        57.90 
TCGA-ZC-AAAA 
       26.93 

$`12Q LOSS 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-5G-A9ZZ TCGA-5K-AAAP 
       14.27        21.99        12.89        68.12        27.45        34.65 
TCGA-5U-AB0D TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB 
       23.47        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-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 
        9.50        14.50        42.15         1.64       125.19        54.08 
TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      150.41        64.83        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-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       84.23        32.25        37.81       112.11        90.05        45.24 
TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A931 
      149.98         4.08       107.80       114.67       120.43        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-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A969 
       23.38        54.15        48.72        42.31        12.46        34.39 
TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H 
       77.39        72.69        64.44        59.80        52.80        49.45 
TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       54.35        50.27         0.46        34.52        24.76        22.19 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       59.31        30.64        28.04        38.30        16.34        68.91 
TCGA-ZT-A8OM 
       45.96 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              5.92               0.46 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             82.65             150.41 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             49.41              40.11 
[1] "5.9 - 82.7 (49.4)"  "0.5 - 150.4 (40.1)"
[1] "hr=" "2.8"
D38V2, continuous
D38V3, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    2  5
  12Q LOSS WILD-TYPE 25 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    5
  12Q LOSS WILD-TYPE   25   91
                      clus
vv                     12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM                2                 25
  THYMUS                              5                 91
[1] 2 2
[1] FALSE
D38V4, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    1  6
  12Q LOSS WILD-TYPE 58 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1    6
  12Q LOSS WILD-TYPE   58   58
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                1                 58
  MALE                  6                 58
[1] 2 2
[1] FALSE
D38V5, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    4  3
  12Q LOSS WILD-TYPE 77 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      4    3
  12Q LOSS WILD-TYPE   77   39
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 4                 77
  YES                3                 39
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  12Q LOSS MUTATED                 1                1                0
  12Q LOSS WILD-TYPE              16               37               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  12Q LOSS MUTATED                  3                2               0
  12Q LOSS WILD-TYPE               27               10              11
D38V6, multiclass
                  clus
vv                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  THYMOMA; TYPE A                 1                 16
  THYMOMA; TYPE AB                1                 37
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                3                 27
  THYMOMA; TYPE B3                2                 10
  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
  12Q LOSS MUTATED       1                         0     6
  12Q LOSS WILD-TYPE    12                         6    96
D38V7, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    6                 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"
D38V8, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    2  5
  12Q LOSS WILD-TYPE  7 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    5
  12Q LOSS WILD-TYPE    7   95
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO                5                 95
[1] 2 2
[1] FALSE

Clustering(39) Variable = 13Q LOSS MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    13   0
  13Q LOSS WILD-TYPE 100   9
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                13                109 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 0                  9 
$`13Q LOSS MUTATED`
TCGA-3S-A8YW TCGA-4V-A9QJ TCGA-4V-A9QX TCGA-4X-A9FD TCGA-5U-AB0E TCGA-XM-A8RC 
       21.14        93.67        14.27        49.41        22.59        97.41 
TCGA-XU-A92X TCGA-XU-A930 TCGA-XU-A932 TCGA-YT-A95D TCGA-YT-A95G TCGA-ZB-A96I 
       77.03        82.65        70.65        24.66        49.78        54.35 
TCGA-ZC-AAAA 
       26.93 

$`13Q LOSS 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-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        18.77        34.52 
TCGA-4V-A9QI TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR 
       96.53        62.73        41.19        31.89        51.68        25.64 
TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4X-A9F9 TCGA-4X-A9FA 
       25.45        26.73        20.61        20.71        21.99        12.89 
TCGA-4X-A9FC TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5V-A9RR TCGA-X7-A8D6 
       68.12        27.45        34.65        23.47        27.19       138.90 
TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE 
       10.68         1.91        65.49        59.11        36.62        32.25 
TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 
       29.62        22.85        23.18         9.50        14.50        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 
        1.64       125.19        54.08       150.41        64.83        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF 
       40.11        52.54        48.92        37.61        13.87        26.20 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O 
       11.93        12.72        84.23        32.25        37.81       112.11 
TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92Y 
       90.05        45.24       149.98         4.08       107.80       114.67 
TCGA-XU-A92Z TCGA-XU-A931 TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXW TCGA-XU-AAXX 
      120.43        52.90        58.82        21.14       123.68        89.46 
TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95E TCGA-YT-A95H 
       62.17        50.53        49.38       107.44        35.18        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-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       49.45        50.27         0.46        34.52        24.76        22.19 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       59.31        30.64        28.04        38.30        16.34        68.91 
TCGA-ZT-A8OM 
       45.96 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             14.27               0.46 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             97.41             150.41 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             49.78              38.30 
[1] "14.3 - 97.4 (49.8)" "0.5 - 150.4 (38.3)"
[1] "hr="   "8e+07"
D39V2, continuous
D39V3, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    5  9
  13Q LOSS WILD-TYPE 22 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      5    9
  13Q LOSS WILD-TYPE   22   87
                      clus
vv                     13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM                5                 22
  THYMUS                              9                 87
[1] 2 2
[1] FALSE
D39V4, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    6  8
  13Q LOSS WILD-TYPE 53 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      6    8
  13Q LOSS WILD-TYPE   53   56
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                6                 53
  MALE                  8                 56
[1] 2 2
[1] FALSE
D39V5, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    7  7
  13Q LOSS WILD-TYPE 74 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      7    7
  13Q LOSS WILD-TYPE   74   35
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 7                 74
  YES                7                 35
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  13Q LOSS MUTATED                 0                4                0
  13Q LOSS WILD-TYPE              17               34               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  13Q LOSS MUTATED                  6                3               1
  13Q LOSS WILD-TYPE               24                9              10
D39V6, multiclass
                  clus
vv                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                4                 34
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                6                 24
  THYMOMA; TYPE B3                3                  9
  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
  13Q LOSS MUTATED       2                         0    12
  13Q LOSS WILD-TYPE    11                         6    90
D39V7, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    2                 11
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                   12                 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"
D39V8, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    3  9
  13Q LOSS WILD-TYPE  6 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3    9
  13Q LOSS WILD-TYPE    6   91
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO                9                 91
[1] 2 2
[1] FALSE

Clustering(40) Variable = 16P LOSS MUTATION ANALYSIS
D40V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     5   0
  16P LOSS WILD-TYPE 108   9
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                117 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 0                  9 
$`16P LOSS MUTATED`
TCGA-3S-A8YW TCGA-XH-A853 TCGA-XU-A930 TCGA-XU-A936 TCGA-ZC-AAAA 
       21.14        40.11        82.65        21.14        26.93 

$`16P LOSS 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-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        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-A8M7 TCGA-X7-A8M8 TCGA-XM-A8R8 TCGA-XM-A8R9 
       54.08       150.41        64.83        83.28        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-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       84.23        32.25        37.81       112.11        90.05        45.24 
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-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY 
       52.90        70.65        58.82       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-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F 
       34.39        77.39        72.69        64.44        59.80        57.90 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O 
       52.80        49.45        54.35        50.27         0.46        34.52 
TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAF 
       24.76        22.19        59.31        30.64        28.04        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       16.34        68.91        45.96 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             21.14               0.46 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             82.65             150.41 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             26.93              42.15 
[1] "21.1 - 82.7 (26.9)" "0.5 - 150.4 (42.1)"
[1] "hr="     "2.6e+07"
D40V2, continuous
D40V3, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    2  3
  16P LOSS WILD-TYPE 25 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2    3
  16P LOSS WILD-TYPE   25   93
                      clus
vv                     16P LOSS MUTATED 16P LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM                2                 25
  THYMUS                              3                 93
[1] 2 2
[1] FALSE
D40V4, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  4
  16P LOSS WILD-TYPE 58 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    4
  16P LOSS WILD-TYPE   58   60
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                1                 58
  MALE                  4                 60
[1] 2 2
[1] FALSE
D40V5, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  4
  16P LOSS WILD-TYPE 80 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    4
  16P LOSS WILD-TYPE   80   38
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 1                 80
  YES                4                 38
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  16P LOSS MUTATED                 0                1                0
  16P LOSS WILD-TYPE              17               37               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  16P LOSS MUTATED                  1                1               2
  16P LOSS WILD-TYPE               29               11               9
D40V6, multiclass
                  clus
vv                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                1                 37
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                1                 29
  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
  16P LOSS MUTATED       0                         1     4
  16P LOSS WILD-TYPE    13                         5    98
D40V7, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                    4                 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"
D40V8, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    2  3
  16P LOSS WILD-TYPE  7 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2    3
  16P LOSS WILD-TYPE    7   97
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO                3                 97
[1] 2 2
[1] FALSE

Clustering(41) Variable = 16Q LOSS MUTATION ANALYSIS
D41V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    11   2
  16Q LOSS WILD-TYPE 102   7
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                13                109 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                  7 
$`16Q LOSS MUTATED`
TCGA-3S-A8YW TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-XH-A853 TCGA-XU-A930 
       21.14        49.41        27.45        23.47        40.11        82.65 
TCGA-XU-A933 TCGA-XU-A936 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96V TCGA-ZC-AAA7 
       58.82        21.14        12.46        34.39        30.64        28.04 
TCGA-ZC-AAAA 
       26.93 

$`16Q LOSS 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-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        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-5K-AAAP TCGA-5U-AB0E TCGA-5V-A9RR 
       21.99        12.89        68.12        34.65        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-A8M7 
       42.15         1.64       125.19        54.08       150.41        64.83 
TCGA-X7-A8M8 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RE 
       83.28        52.54        48.92        37.61        97.41        13.87 
TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       26.20        11.93        12.72        84.23        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-A931 TCGA-XU-A932 TCGA-XU-AAXW 
       77.03       114.67       120.43        52.90        70.65       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-A962 TCGA-ZB-A963 
       35.18        49.78        23.38         5.92        54.15        48.72 
TCGA-ZB-A964 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F 
       42.31        77.39        72.69        64.44        59.80        57.90 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O 
       52.80        49.45        54.35        50.27         0.46        34.52 
TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       24.76        22.19        59.31        38.30        16.34        68.91 
TCGA-ZT-A8OM 
       45.96 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             12.46               0.46 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             82.65             150.41 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             28.04              45.24 
[1] "12.5 - 82.7 (28.0)" "0.5 - 150.4 (45.2)"
[1] "hr=" "4.2"
D41V2, continuous
D41V3, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    4  9
  16Q LOSS WILD-TYPE 23 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4    9
  16Q LOSS WILD-TYPE   23   87
                      clus
vv                     16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM                4                 23
  THYMUS                              9                 87
[1] 2 2
[1] FALSE
D41V4, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    7  6
  16Q LOSS WILD-TYPE 52 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      7    6
  16Q LOSS WILD-TYPE   52   58
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                7                 52
  MALE                  6                 58
[1] 2 2
[1] FALSE
D41V5, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    6  7
  16Q LOSS WILD-TYPE 75 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      6    7
  16Q LOSS WILD-TYPE   75   35
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 6                 75
  YES                7                 35
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  16Q LOSS MUTATED                 0                1                0
  16Q LOSS WILD-TYPE              17               37               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  16Q LOSS MUTATED                  2                1               9
  16Q LOSS WILD-TYPE               28               11               2
D41V6, multiclass
                  clus
vv                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                1                 37
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                2                 28
  THYMOMA; TYPE B3                1                 11
  THYMOMA; TYPE C                 9                  2
[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
  16Q LOSS MUTATED       1                         1    11
  16Q LOSS WILD-TYPE    12                         5    91
D41V7, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   11                 91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    3 10
  16Q LOSS WILD-TYPE  6 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3   10
  16Q LOSS WILD-TYPE    6   90
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO               10                 90
[1] 2 2
[1] FALSE

Clustering(42) Variable = 17P LOSS MUTATION ANALYSIS
D42V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    13   1
  17P LOSS WILD-TYPE 100   8
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                14                108 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 1                  8 
$`17P LOSS MUTATED`
TCGA-XM-A8RG TCGA-3S-A8YW TCGA-4V-A9QJ TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0D 
       12.69        21.14        93.67        49.41        27.45        23.47 
TCGA-5U-AB0E TCGA-XU-A92X TCGA-XU-A933 TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A96F 
       22.59        77.03        58.82         5.92        54.15        57.90 
TCGA-ZB-A96L TCGA-ZC-AAAA 
       50.27        26.93 

$`17P LOSS 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-AAYX TCGA-3T-AA9L TCGA-4V-A9QI 
       81.80        25.48        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-5K-AAAP TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 
       68.12        34.65        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-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
       54.08       150.41        64.83        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-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R 
       12.72        84.23        32.25        37.81       112.11        90.05 
TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92Y TCGA-XU-A92Z 
       45.24       149.98         4.08       107.80       114.67       120.43 
TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A936 TCGA-XU-AAXW TCGA-XU-AAXX 
       82.65        52.90        70.65        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-A963 TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A969 
       49.78        23.38        48.72        42.31        12.46        34.39 
TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H 
       77.39        72.69        64.44        59.80        52.80        49.45 
TCGA-ZB-A96I TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
       54.35         0.46        34.52        24.76        22.19        59.31 
TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       30.64        28.04        38.30        16.34        68.91        45.96 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              5.92               0.46 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             93.67             150.41 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             38.43              40.65 
[1] "5.9 - 93.7 (38.4)"  "0.5 - 150.4 (40.6)"
[1] "hr=" "1.5"
D42V2, continuous
D42V3, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    3 11
  17P LOSS WILD-TYPE 24 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3   11
  17P LOSS WILD-TYPE   24   85
                      clus
vv                     17P LOSS MUTATED 17P LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM                3                 24
  THYMUS                             11                 85
[1] 2 2
[1] FALSE
D42V4, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    5  9
  17P LOSS WILD-TYPE 54 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      5    9
  17P LOSS WILD-TYPE   54   55
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                5                 54
  MALE                  9                 55
[1] 2 2
[1] FALSE
D42V5, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    8  6
  17P LOSS WILD-TYPE 73 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      8    6
  17P LOSS WILD-TYPE   73   36
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 8                 73
  YES                6                 36
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  17P LOSS MUTATED                 3                1                0
  17P LOSS WILD-TYPE              14               37               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  17P LOSS MUTATED                  3                3               4
  17P LOSS WILD-TYPE               27                9               7
D42V6, multiclass
                  clus
vv                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  THYMOMA; TYPE A                 3                 14
  THYMOMA; TYPE AB                1                 37
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                3                 27
  THYMOMA; TYPE B3                3                  9
  THYMOMA; TYPE C                 4                  7
[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
  17P LOSS MUTATED       2                         0    12
  17P LOSS WILD-TYPE    11                         6    90
D42V7, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    2                 11
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                   12                 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"
D42V8, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    4 10
  17P LOSS WILD-TYPE  5 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4   10
  17P LOSS WILD-TYPE    5   90
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO               10                 90
[1] 2 2
[1] FALSE

Clustering(43) Variable = 17Q LOSS MUTATION ANALYSIS
D43V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED     6   0
  17Q LOSS WILD-TYPE 107   9
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 6                116 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 0                  9 
$`17Q LOSS MUTATED`
TCGA-3S-A8YW TCGA-4X-A9FD TCGA-5U-AB0E TCGA-XU-A92X TCGA-ZB-A96L TCGA-ZC-AAAA 
       21.14        49.41        22.59        77.03        50.27        26.93 

$`17Q LOSS 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-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        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-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D 
       21.99        12.89        68.12        27.45        34.65        23.47 
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-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       64.83        83.28        40.11        52.54        48.92        37.61 
TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
       97.41        13.87        26.20        11.93        12.72        84.23 
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-A92Y TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 
        4.08       107.80       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-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F 
       34.39        77.39        72.69        64.44        59.80        57.90 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
       52.80        49.45        54.35         0.46        34.52        24.76 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH 
       22.19        59.31        30.64        28.04        38.30        16.34 
TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       68.91        45.96 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             21.14               0.46 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             77.03             150.41 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             38.17              40.65 
[1] "21.1 - 77.0 (38.2)" "0.5 - 150.4 (40.6)"
[1] "hr="     "2.6e+07"
D43V2, continuous
D43V3, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    2  4
  17Q LOSS WILD-TYPE 25 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    4
  17Q LOSS WILD-TYPE   25   92
                      clus
vv                     17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM                2                 25
  THYMUS                              4                 92
[1] 2 2
[1] FALSE
D43V4, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    2  4
  17Q LOSS WILD-TYPE 57 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    4
  17Q LOSS WILD-TYPE   57   60
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                2                 57
  MALE                  4                 60
[1] 2 2
[1] FALSE
D43V5, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    3  3
  17Q LOSS WILD-TYPE 78 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3    3
  17Q LOSS WILD-TYPE   78   39
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 3                 78
  YES                3                 39
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  17Q LOSS MUTATED                 0                0                0
  17Q LOSS WILD-TYPE              17               38               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  17Q LOSS MUTATED                  3                2               1
  17Q LOSS WILD-TYPE               27               10              10
D43V6, multiclass
                  clus
vv                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                0                 38
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                3                 27
  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
  17Q LOSS MUTATED       1                         0     5
  17Q LOSS WILD-TYPE    12                         6    97
D43V7, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    5                 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"
D43V8, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    3  3
  17Q LOSS WILD-TYPE  6 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3    3
  17Q LOSS WILD-TYPE    6   97
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO                3                 97
[1] 2 2
[1] FALSE

Clustering(44) Variable = 18P LOSS MUTATION ANALYSIS
D44V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED     5   2
  18P LOSS WILD-TYPE 108   7
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                115 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                  7 
$`18P LOSS MUTATED`
TCGA-XM-A8RD TCGA-4X-A9FD TCGA-5U-AB0D TCGA-5U-AB0E TCGA-XU-A930 TCGA-XU-A931 
       50.83        49.41        23.47        22.59        82.65        52.90 
TCGA-ZB-A961 
        5.92 

$`18P LOSS WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RG TCGA-XM-AAZ1 TCGA-XU-A92Q 
       95.67        23.57        15.09        12.69        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-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-5G-A9ZZ TCGA-5K-AAAP TCGA-5V-A9RR 
       21.99        12.89        68.12        27.45        34.65        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-A8M7 
       42.15         1.64       125.19        54.08       150.41        64.83 
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-A8RL TCGA-XM-AAZ2 
       13.87        26.20        11.93        12.72        84.23        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
       37.81       112.11        90.05        45.24       149.98         4.08 
TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A932 TCGA-XU-A933 
      107.80        77.03       114.67       120.43        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-A95D TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A962 
      107.44        24.66        35.18        49.78        23.38        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-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
       50.27         0.46        34.52        24.76        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 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              5.92               0.46 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             82.65             150.41 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             49.41              40.11 
[1] "5.9 - 82.7 (49.4)"  "0.5 - 150.4 (40.1)"
[1] "hr=" "7.3"
D44V2, continuous
D44V3, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2  5
  18P LOSS WILD-TYPE 25 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    5
  18P LOSS WILD-TYPE   25   91
                      clus
vv                     18P LOSS MUTATED 18P LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM                2                 25
  THYMUS                              5                 91
[1] 2 2
[1] FALSE
D44V4, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    4  3
  18P LOSS WILD-TYPE 55 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4    3
  18P LOSS WILD-TYPE   55   61
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                4                 55
  MALE                  3                 61
[1] 2 2
[1] FALSE
D44V5, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    4  3
  18P LOSS WILD-TYPE 77 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4    3
  18P LOSS WILD-TYPE   77   39
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 4                 77
  YES                3                 39
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  18P LOSS MUTATED                 1                0                0
  18P LOSS WILD-TYPE              16               38               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  18P LOSS MUTATED                  2                3               1
  18P LOSS WILD-TYPE               28                9              10
D44V6, multiclass
                  clus
vv                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  THYMOMA; TYPE A                 1                 16
  THYMOMA; TYPE AB                0                 38
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                2                 28
  THYMOMA; TYPE B3                3                  9
  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
  18P LOSS MUTATED       0                         0     7
  18P LOSS WILD-TYPE    13                         6    95
D44V7, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    7                 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"
D44V8, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2  4
  18P LOSS WILD-TYPE  7 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    4
  18P LOSS WILD-TYPE    7   96
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO                4                 96
[1] 2 2
[1] FALSE

Clustering(45) Variable = 18Q LOSS MUTATION ANALYSIS
D45V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED     5   2
  18Q LOSS WILD-TYPE 108   7
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                115 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                  7 
$`18Q LOSS MUTATED`
TCGA-XM-A8RD TCGA-4X-A9FD TCGA-5U-AB0D TCGA-5U-AB0E TCGA-XU-A930 TCGA-XU-A931 
       50.83        49.41        23.47        22.59        82.65        52.90 
TCGA-ZB-A961 
        5.92 

$`18Q LOSS WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RG TCGA-XM-AAZ1 TCGA-XU-A92Q 
       95.67        23.57        15.09        12.69        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-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-5G-A9ZZ TCGA-5K-AAAP TCGA-5V-A9RR 
       21.99        12.89        68.12        27.45        34.65        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-A8M7 
       42.15         1.64       125.19        54.08       150.41        64.83 
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-A8RL TCGA-XM-AAZ2 
       13.87        26.20        11.93        12.72        84.23        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
       37.81       112.11        90.05        45.24       149.98         4.08 
TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A932 TCGA-XU-A933 
      107.80        77.03       114.67       120.43        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-A95D TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A962 
      107.44        24.66        35.18        49.78        23.38        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-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
       50.27         0.46        34.52        24.76        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 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              5.92               0.46 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             82.65             150.41 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             49.41              40.11 
[1] "5.9 - 82.7 (49.4)"  "0.5 - 150.4 (40.1)"
[1] "hr=" "7.3"
D45V2, continuous
D45V3, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    2  5
  18Q LOSS WILD-TYPE 25 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2    5
  18Q LOSS WILD-TYPE   25   91
                      clus
vv                     18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM                2                 25
  THYMUS                              5                 91
[1] 2 2
[1] FALSE
D45V4, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    4  3
  18Q LOSS WILD-TYPE 55 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4    3
  18Q LOSS WILD-TYPE   55   61
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                4                 55
  MALE                  3                 61
[1] 2 2
[1] FALSE
D45V5, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    4  3
  18Q LOSS WILD-TYPE 77 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4    3
  18Q LOSS WILD-TYPE   77   39
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 4                 77
  YES                3                 39
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  18Q LOSS MUTATED                 1                0                0
  18Q LOSS WILD-TYPE              16               38               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  18Q LOSS MUTATED                  2                3               1
  18Q LOSS WILD-TYPE               28                9              10
D45V6, multiclass
                  clus
vv                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  THYMOMA; TYPE A                 1                 16
  THYMOMA; TYPE AB                0                 38
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                2                 28
  THYMOMA; TYPE B3                3                  9
  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
  18Q LOSS MUTATED       0                         0     7
  18Q LOSS WILD-TYPE    13                         6    95
D45V7, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    7                 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"
D45V8, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    2  4
  18Q LOSS WILD-TYPE  7 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2    4
  18Q LOSS WILD-TYPE    7   96
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO                4                 96
[1] 2 2
[1] FALSE

Clustering(46) Variable = 19P LOSS MUTATION ANALYSIS
D46V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED     3   0
  19P LOSS WILD-TYPE 110   9
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                119 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 0                  9 
$`19P LOSS MUTATED`
TCGA-3S-A8YW TCGA-5U-AB0D TCGA-XU-A936 
       21.14        23.47        21.14 

$`19P LOSS 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-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        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-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-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 
        9.50        14.50        42.15         1.64       125.19        54.08 
TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      150.41        64.83        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-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       84.23        32.25        37.81       112.11        90.05        45.24 
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-AAXW TCGA-XU-AAXX 
       82.65        52.90        70.65        58.82       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-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46        34.39        77.39        72.69        64.44        59.80 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M 
       57.90        52.80        49.45        54.35        50.27         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
       34.52        24.76        22.19        59.31        30.64        28.04 
TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       26.93        38.30        16.34        68.91        45.96 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             21.14               0.46 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             23.47             150.41 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             21.14              42.15 
[1] "21.1 - 23.5 (21.1)" "0.5 - 150.4 (42.1)"
[1] "hr="     "9300000"
D46V2, continuous
D46V3, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    2  1
  19P LOSS WILD-TYPE 25 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    1
  19P LOSS WILD-TYPE   25   95
                      clus
vv                     19P LOSS MUTATED 19P LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM                2                 25
  THYMUS                              1                 95
[1] 2 2
[1] FALSE
D46V4, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    2  1
  19P LOSS WILD-TYPE 57 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    1
  19P LOSS WILD-TYPE   57   63
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                2                 57
  MALE                  1                 63
[1] 2 2
[1] FALSE
D46V5, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    1  2
  19P LOSS WILD-TYPE 80 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1    2
  19P LOSS WILD-TYPE   80   40
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 1                 80
  YES                2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  19P LOSS MUTATED                 0                0                0
  19P LOSS WILD-TYPE              17               38               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  19P LOSS MUTATED                  0                0               3
  19P LOSS WILD-TYPE               30               12               8
D46V6, multiclass
                  clus
vv                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                0                 38
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                0                 30
  THYMOMA; TYPE B3                0                 12
  THYMOMA; TYPE C                 3                  8
[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
  19P LOSS MUTATED       0                         0     3
  19P LOSS WILD-TYPE    13                         6    99
D46V7, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    2  1
  19P LOSS WILD-TYPE  7 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    1
  19P LOSS WILD-TYPE    7   99
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO                1                 99
[1] 2 2
[1] FALSE

Clustering(47) Variable = 19Q LOSS MUTATION ANALYSIS
D47V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED     3   0
  19Q LOSS WILD-TYPE 110   9
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                119 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 0                  9 
$`19Q LOSS MUTATED`
TCGA-3S-A8YW TCGA-5U-AB0D TCGA-XU-A936 
       21.14        23.47        21.14 

$`19Q LOSS 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-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        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-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-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 
        9.50        14.50        42.15         1.64       125.19        54.08 
TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      150.41        64.83        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-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       84.23        32.25        37.81       112.11        90.05        45.24 
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-AAXW TCGA-XU-AAXX 
       82.65        52.90        70.65        58.82       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-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46        34.39        77.39        72.69        64.44        59.80 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M 
       57.90        52.80        49.45        54.35        50.27         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
       34.52        24.76        22.19        59.31        30.64        28.04 
TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       26.93        38.30        16.34        68.91        45.96 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             21.14               0.46 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             23.47             150.41 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             21.14              42.15 
[1] "21.1 - 23.5 (21.1)" "0.5 - 150.4 (42.1)"
[1] "hr="     "9300000"
D47V2, continuous
D47V3, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2  1
  19Q LOSS WILD-TYPE 25 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    1
  19Q LOSS WILD-TYPE   25   95
                      clus
vv                     19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM                2                 25
  THYMUS                              1                 95
[1] 2 2
[1] FALSE
D47V4, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2  1
  19Q LOSS WILD-TYPE 57 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    1
  19Q LOSS WILD-TYPE   57   63
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                2                 57
  MALE                  1                 63
[1] 2 2
[1] FALSE
D47V5, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    1  2
  19Q LOSS WILD-TYPE 80 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    2
  19Q LOSS WILD-TYPE   80   40
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 1                 80
  YES                2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  19Q LOSS MUTATED                 0                0                0
  19Q LOSS WILD-TYPE              17               38               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  19Q LOSS MUTATED                  0                0               3
  19Q LOSS WILD-TYPE               30               12               8
D47V6, multiclass
                  clus
vv                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                0                 38
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                0                 30
  THYMOMA; TYPE B3                0                 12
  THYMOMA; TYPE C                 3                  8
[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
  19Q LOSS MUTATED       0                         0     3
  19Q LOSS WILD-TYPE    13                         6    99
D47V7, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2  1
  19Q LOSS WILD-TYPE  7 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    1
  19Q LOSS WILD-TYPE    7   99
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO                1                 99
[1] 2 2
[1] FALSE

Clustering(48) Variable = 21Q LOSS MUTATION ANALYSIS
D48V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED     9   0
  21Q LOSS WILD-TYPE 104   9
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 9                113 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 0                  9 
$`21Q LOSS MUTATED`
TCGA-4V-A9QR TCGA-4X-A9FD TCGA-5U-AB0D TCGA-5U-AB0E TCGA-XU-A92X TCGA-XU-A930 
       25.64        49.41        23.47        22.59        77.03        82.65 
TCGA-ZB-A96F TCGA-ZB-A96I TCGA-ZC-AAAA 
       57.90        54.35        26.93 

$`21Q LOSS 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-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       51.68        25.45        26.73        20.61        20.71        14.27 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5V-A9RR 
       21.99        12.89        68.12        27.45        34.65        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-A8M7 
       42.15         1.64       125.19        54.08       150.41        64.83 
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-A8RL TCGA-XM-AAZ2 
       13.87        26.20        11.93        12.72        84.23        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
       37.81       112.11        90.05        45.24       149.98         4.08 
TCGA-XU-A92W TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 
      107.80       114.67       120.43        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-A95D TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 
      107.44        24.66        35.18        49.78        23.38         5.92 
TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A 
       54.15        48.72        42.31        12.46        34.39        77.39 
TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96L 
       72.69        64.44        59.80        52.80        49.45        50.27 
TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V 
        0.46        34.52        24.76        22.19        59.31        30.64 
TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       28.04        38.30        16.34        68.91        45.96 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             22.59               0.46 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             82.65             150.41 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             49.41              40.11 
[1] "22.6 - 82.7 (49.4)" "0.5 - 150.4 (40.1)"
[1] "hr="     "7.5e+07"
D48V2, continuous
D48V3, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    4  5
  21Q LOSS WILD-TYPE 23 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4    5
  21Q LOSS WILD-TYPE   23   91
                      clus
vv                     21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM                4                 23
  THYMUS                              5                 91
[1] 2 2
[1] FALSE
D48V4, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    4  5
  21Q LOSS WILD-TYPE 55 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4    5
  21Q LOSS WILD-TYPE   55   59
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                4                 55
  MALE                  5                 59
[1] 2 2
[1] FALSE
D48V5, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    5  4
  21Q LOSS WILD-TYPE 76 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5    4
  21Q LOSS WILD-TYPE   76   38
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 5                 76
  YES                4                 38
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  21Q LOSS MUTATED                 0                2                0
  21Q LOSS WILD-TYPE              17               36               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  21Q LOSS MUTATED                  3                3               1
  21Q LOSS WILD-TYPE               27                9              10
D48V6, multiclass
                  clus
vv                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  THYMOMA; TYPE A                 0                 17
  THYMOMA; TYPE AB                2                 36
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                3                 27
  THYMOMA; TYPE B3                3                  9
  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
  21Q LOSS MUTATED       1                         0     8
  21Q LOSS WILD-TYPE    12                         6    94
D48V7, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    8                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    3  6
  21Q LOSS WILD-TYPE  6 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3    6
  21Q LOSS WILD-TYPE    6   94
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO                6                 94
[1] 2 2
[1] FALSE

Clustering(49) Variable = 22Q LOSS MUTATION ANALYSIS
D49V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    12   1
  22Q LOSS WILD-TYPE 101   8
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                13                109 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                  8 
$`22Q LOSS MUTATED`
TCGA-3G-AB19 TCGA-5U-AB0F TCGA-3S-A8YW TCGA-4V-A9QJ TCGA-4V-A9QN TCGA-4V-A9QX 
       95.67        15.09        21.14        93.67        31.89        14.27 
TCGA-5U-AB0D TCGA-XM-A8RC TCGA-XU-A92Z TCGA-XU-A936 TCGA-ZB-A963 TCGA-ZB-A96A 
       23.47        97.41       120.43        21.14        48.72        77.39 
TCGA-ZT-A8OM 
       45.96 

$`22Q LOSS WILD-TYPE`
TCGA-4X-A9FB TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-AAZ1 TCGA-XU-A92Q TCGA-YT-A95F 
       23.57        50.83        12.69        13.05        35.90        25.48 
TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T 
       26.83        71.11        45.63        68.58        59.15        81.80 
TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QL 
       25.48        15.35        18.77        34.52        96.53        62.73 
TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       41.19        51.68        25.64        25.45        26.73        20.61 
TCGA-4V-A9QW TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ 
       20.71        21.99        12.89        68.12        49.41        27.45 
TCGA-5K-AAAP TCGA-5U-AB0E TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 
       34.65        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-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
       54.08       150.41        64.83        83.28        40.11        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI 
       48.92        37.61        13.87        26.20        11.93        12.72 
TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       84.23        32.25        37.81       112.11        90.05        45.24 
TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A930 
      149.98         4.08       107.80        77.03       114.67        82.65 
TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY 
       52.90        70.65        58.82       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-A964 TCGA-ZB-A966 TCGA-ZB-A969 
       23.38         5.92        54.15        42.31        12.46        34.39 
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-A96P TCGA-ZB-A96Q 
       54.35        50.27         0.46        34.52        24.76        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 
       68.91 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             14.27               0.46 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            120.43             150.41 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             45.96              40.11 
[1] "14.3 - 120.4 (46.0)" "0.5 - 150.4 (40.1)" 
[1] "hr=" "1.3"
D49V2, continuous
D49V3, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    5  8
  22Q LOSS WILD-TYPE 22 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      5    8
  22Q LOSS WILD-TYPE   22   88
                      clus
vv                     22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM                5                 22
  THYMUS                              8                 88
[1] 2 2
[1] FALSE
D49V4, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    7  6
  22Q LOSS WILD-TYPE 52 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      7    6
  22Q LOSS WILD-TYPE   52   58
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                7                 52
  MALE                  6                 58
[1] 2 2
[1] FALSE
D49V5, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    5  8
  22Q LOSS WILD-TYPE 76 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      5    8
  22Q LOSS WILD-TYPE   76   34
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 5                 76
  YES                8                 34
[1] 2 2
[1] FALSE
                    vv
clus                 THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  22Q LOSS MUTATED                 2                3                0
  22Q LOSS WILD-TYPE              15               35               15
                    vv
clus                 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  22Q LOSS MUTATED                  2                2               4
  22Q LOSS WILD-TYPE               28               10               7
D49V6, multiclass
                  clus
vv                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  THYMOMA; TYPE A                 2                 15
  THYMOMA; TYPE AB                3                 35
  THYMOMA; TYPE B1                0                 15
  THYMOMA; TYPE B2                2                 28
  THYMOMA; TYPE B3                2                 10
  THYMOMA; TYPE C                 4                  7
[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
  22Q LOSS MUTATED       1                         0    12
  22Q LOSS WILD-TYPE    12                         6    90
D49V7, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                   12                 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"
D49V8, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    4  9
  22Q LOSS WILD-TYPE  5 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4    9
  22Q LOSS WILD-TYPE    5   91
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO                9                 91
[1] 2 2
[1] FALSE

Clustering(50) Variable = XP LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED     6   2
  XP LOSS WILD-TYPE 107   7
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                8               114 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                2                 7 
$`XP LOSS MUTATED`
TCGA-3G-AB0T TCGA-3S-A8YW TCGA-4V-A9QJ TCGA-4V-A9QN TCGA-4X-A9FD TCGA-XU-A931 
       81.80        21.14        93.67        31.89        49.41        52.90 
TCGA-ZB-A96F TCGA-ZB-A96I 
       57.90        54.35 

$`XP LOSS 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-AB14 TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI 
       59.15        25.48        15.35        18.77        34.52        96.53 
TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT 
       62.73        41.19        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-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5V-A9RR TCGA-X7-A8D6 
       27.45        34.65        23.47        22.59        27.19       138.90 
TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE 
       10.68         1.91        65.49        59.11        36.62        32.25 
TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 
       29.62        22.85        23.18         9.50        14.50        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 
        1.64       125.19        54.08       150.41        64.83        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-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       26.20        11.93        12.72        84.23        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-A932 TCGA-XU-A933 
       77.03       114.67       120.43        82.65        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-A95D TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 
      107.44        24.66        35.18        49.78        23.38         5.92 
TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A 
       54.15        48.72        42.31        12.46        34.39        77.39 
TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96L 
       72.69        64.44        59.80        52.80        49.45        50.27 
TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V 
        0.46        34.52        24.76        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 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
            21.14              0.46 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            93.67            150.41 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           53.625            38.055 
[1] "21.1 - 93.7 (53.6)" "0.5 - 150.4 (38.1)"
[1] "hr=" "4.4"
D50V2, continuous
D50V3, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    2  6
  XP LOSS WILD-TYPE 25 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2    6
  XP LOSS WILD-TYPE   25   90
                      clus
vv                     XP LOSS MUTATED XP LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM               2                25
  THYMUS                             6                90
[1] 2 2
[1] FALSE
D50V4, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    4  4
  XP LOSS WILD-TYPE 55 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      4    4
  XP LOSS WILD-TYPE   55   60
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE               4                55
  MALE                 4                60
[1] 2 2
[1] FALSE
D50V5, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    3  5
  XP LOSS WILD-TYPE 78 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      3    5
  XP LOSS WILD-TYPE   78   37
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO                3                78
  YES               5                37
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  XP LOSS MUTATED                 0                2                1
  XP LOSS WILD-TYPE              17               36               14
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  XP LOSS MUTATED                  1                3               1
  XP LOSS WILD-TYPE               29                9              10
D50V6, multiclass
                  clus
vv                 XP LOSS MUTATED XP LOSS WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               2                36
  THYMOMA; TYPE B1               1                14
  THYMOMA; TYPE B2               1                29
  THYMOMA; TYPE B3               3                 9
  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
  XP LOSS MUTATED       0                         0     8
  XP LOSS WILD-TYPE    13                         6    94
D50V7, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   8                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    2  5
  XP LOSS WILD-TYPE  7 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2    5
  XP LOSS WILD-TYPE    7   95
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO               5                95
[1] 2 2
[1] FALSE

Clustering(51) Variable = XQ LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED     4   1
  XQ LOSS WILD-TYPE 109   8
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5               117 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                 8 
$`XQ LOSS MUTATED`
TCGA-3S-A8YW TCGA-4V-A9QN TCGA-4X-A9FD TCGA-XU-A931 TCGA-ZB-A96I 
       21.14        31.89        49.41        52.90        54.35 

$`XQ LOSS 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-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        18.77        34.52 
TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QR 
       96.53        93.67        62.73        41.19        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-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E 
       12.89        68.12        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-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       64.83        83.28        40.11        52.54        48.92        37.61 
TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
       97.41        13.87        26.20        11.93        12.72        84.23 
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-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-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F 
       34.39        77.39        72.69        64.44        59.80        57.90 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
       52.80        49.45        50.27         0.46        34.52        24.76 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
       22.19        59.31        30.64        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       16.34        68.91        45.96 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            21.14              0.46 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            54.35            150.41 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            49.41             40.11 
[1] "21.1 - 54.4 (49.4)" "0.5 - 150.4 (40.1)"
[1] "hr=" "4.2"
D51V2, continuous
D51V3, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    1  4
  XQ LOSS WILD-TYPE 26 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    4
  XQ LOSS WILD-TYPE   26   92
                      clus
vv                     XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ANTERIOR MEDIASTINUM               1                26
  THYMUS                             4                92
[1] 2 2
[1] FALSE
D51V4, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    4  1
  XQ LOSS WILD-TYPE 55 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4    1
  XQ LOSS WILD-TYPE   55   63
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               4                55
  MALE                 1                63
[1] 2 2
[1] FALSE
D51V5, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    2  3
  XQ LOSS WILD-TYPE 79 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2    3
  XQ LOSS WILD-TYPE   79   39
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                2                79
  YES               3                39
[1] 2 2
[1] FALSE
                   vv
clus                THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  XQ LOSS MUTATED                 0                1                0
  XQ LOSS WILD-TYPE              17               37               15
                   vv
clus                THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  XQ LOSS MUTATED                  1                2               1
  XQ LOSS WILD-TYPE               29               10              10
D51V6, multiclass
                  clus
vv                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  THYMOMA; TYPE A                0                17
  THYMOMA; TYPE AB               1                37
  THYMOMA; TYPE B1               0                15
  THYMOMA; TYPE B2               1                29
  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
  XQ LOSS MUTATED       0                         0     5
  XQ LOSS WILD-TYPE    13                         6    97
D51V7, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   5                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"
D51V8, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    2  2
  XQ LOSS WILD-TYPE  7 98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2    2
  XQ LOSS WILD-TYPE    7   98
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO               2                98
[1] 2 2
[1] FALSE
