[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/15092844/THYM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THYM-TP/15104466/transformed.cor.cli.txt"

nPatients in clinical file=122, in cluster file=123, common to both=121
[1] "Reduce the number of clustering variables from 82 to 52."
[1]  52 121
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8               113 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8               113 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               22                99 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               22                99 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5               116 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5               116 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11               110 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11               110 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9               112 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9               112 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               16               105 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               16               105 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               16               105 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               16               105 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12               109 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12               109 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               12               109 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               12               109 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               11               110 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               11               110 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               11               110 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               11               110 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                117 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                117 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                117 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                117 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                13                108 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                13                108 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                12                109 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                12                109 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                114 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                114 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                118 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                118 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                118 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                118 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                118 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                118 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                118 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                118 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                10                111 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                10                111 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                111 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                111 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                118 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                118 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                116 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                116 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                3               118 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                3               118 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                5               116 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                5               116 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4               117 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4               117 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               12               109 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               12               109 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                7               114 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                7               114 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                5               116 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                5               116 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4               117 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4               117 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               20               101 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               20               101 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               19               102 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               19               102 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                4               117 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                4               117 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 3                118 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 3                118 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 9                112 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 9                112 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                114 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                114 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 8                113 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 8                113 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 7                114 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 7                114 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                107 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                107 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                116 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                116 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                13                108 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                13                108 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                14                107 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                14                107 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 6                115 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 6                115 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                114 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                114 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                114 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                114 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                118 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                118 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                118 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                118 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 9                112 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 9                112 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                13                108 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                13                108 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                7               114 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                7               114 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4               117 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4               117 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "NEOPLASM_DISEASESTAGE"                 
 [6] "PATHOLOGY_T_STAGE"                     
 [7] "PATHOLOGY_N_STAGE"                     
 [8] "PATHOLOGY_M_STAGE"                     
 [9] "DCC_UPLOAD_DATE"                       
[10] "GENDER"                                
[11] "RADIATION_THERAPY"                     
[12] "RADIATIONS_RADIATION_REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCH_NUMBER"                          

Input Data has 15 rows and 121 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=110,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NEOPLASM_DISEASESTAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'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 7:'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 8:'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 9:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH_NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 121 columns, 1 survival variables, and 4 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH" "GENDER"         "RACE"           "ETHNICITY"     
YEARS_TO_BIRTH, nv=48, binary=FALSE, numeric=TRUE
GENDER, nv=2, 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     6   2
  1P GAIN WILD-TYPE 107   4
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8               111 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                 4 
$`1P GAIN MUTATED`
TCGA-3G-AB0T TCGA-3S-A8YW TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-XU-A92Y TCGA-XU-A932 
       81.80        13.48        19.50        11.57       114.67        70.65 
TCGA-YT-A95G TCGA-ZB-A96I 
       49.78         5.19 

$`1P GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-AAYX 
       56.65        59.15        17.75        90.61        15.35         9.96 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN 
       34.52        89.23        88.83        56.75        38.50        28.90 
TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW 
       45.07        19.76        19.76        21.70        16.60        14.07 
TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-4X-A9FD 
       11.24        15.78        12.89        23.57        55.46        39.45 
TCGA-5K-AAAP TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 
       34.65        10.36        15.09        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        49.22        36.62        32.25        29.62 
TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 
       22.85        23.18         2.37        14.50        42.15         1.64 
TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      125.19        54.08        83.28        30.08        52.54        48.92 
TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG 
       37.61        97.41        50.83         7.69        26.20        12.69 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       11.93        12.72        84.23        13.05        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
      112.11        35.90        90.05        45.24       149.98         4.08 
TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A933 
      107.80        77.03       120.43        82.65        52.90        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-A95F TCGA-YT-A95H TCGA-ZB-A961 
      107.44        18.67        13.32        22.78        12.79         0.13 
TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 
        0.20        30.74        18.58        16.57        12.46         0.66 
TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F 
       10.68        60.33        43.43        42.81         0.23         0.16 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O 
       32.35        37.48        31.50         0.30         0.46         1.81 
TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       10.68         7.17        35.34         8.52        28.04        26.93 
TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       38.30        16.34        68.91 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             5.19              0.13 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           114.67            149.98 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            34.64             30.74 
[1] "5.2 - 114.7 (34.6)" "0.1 - 150.0 (30.7)"
[1] "hr=" "5"  
D1V2, continuous
D1V3, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    5  3
  1P GAIN WILD-TYPE 54 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      5    3
  1P GAIN WILD-TYPE   54   59
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               5                54
  MALE                 3                59
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       1                         0     7
  1P GAIN WILD-TYPE    12                         6    93
D1V4, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   7                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    2  5
  1P GAIN WILD-TYPE  7 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2    5
  1P GAIN WILD-TYPE    7   93
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO               5                93
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   17  5
  1Q GAIN WILD-TYPE 96  1
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               22                97 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                5                 1 
$`1Q GAIN MUTATED`
TCGA-3G-AB0T TCGA-3S-A8YW TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4X-A9FD TCGA-5G-A9ZZ 
       81.80        13.48        19.76        19.76        39.45        19.50 
TCGA-5U-AB0D TCGA-X7-A8M3 TCGA-XM-A8RD TCGA-XM-AAZ1 TCGA-XU-A92Y TCGA-XU-A930 
       11.57         1.64        50.83        13.05       114.67        82.65 
TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A936 TCGA-YT-A95G TCGA-ZB-A961 TCGA-ZB-A966 
       52.90        70.65        21.14        49.78         0.13        12.46 
TCGA-ZB-A96F TCGA-ZB-A96I TCGA-ZB-A96V TCGA-ZC-AAA7 
        0.16         5.19         8.52        28.04 

$`1Q GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-AAYX 
       56.65        59.15        17.75        90.61        15.35         9.96 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN 
       34.52        89.23        88.83        56.75        38.50        28.90 
TCGA-4V-A9QQ TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 
       45.07        21.70        16.60        14.07        11.24        15.78 
TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-5K-AAAP TCGA-5U-AB0E TCGA-5U-AB0F 
       12.89        23.57        55.46        34.65        10.36        15.09 
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        49.22 
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         2.37 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       14.50        42.15       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF 
       52.54        48.92        37.61        97.41         7.69        26.20 
TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       12.69        11.93        12.72        84.23        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
      112.11        35.90        90.05        45.24       149.98         4.08 
TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Z TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX 
      107.80        77.03       120.43        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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95H TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 
       22.78        12.79         0.20        30.74        18.58        16.57 
TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E 
        0.66        10.68        60.33        43.43        42.81         0.23 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O 
       32.35        37.48        31.50         0.30         0.46         1.81 
TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
       10.68         7.17        35.34        26.93        38.30        16.34 
TCGA-ZL-A9V6 
       68.91 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.13              0.20 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           114.67            149.98 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            19.76             32.25 
[1] "0.1 - 114.7 (19.8)" "0.2 - 150.0 (32.2)"
[1] "hr=" "26" 
D2V2, continuous
D2V3, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   13  9
  1Q GAIN WILD-TYPE 46 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     13    9
  1Q GAIN WILD-TYPE   46   53
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              13                46
  MALE                 9                53
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       1                         0    21
  1Q GAIN WILD-TYPE    12                         6    79
D2V4, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  21                79
[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"
D2V5, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    2 18
  1Q GAIN WILD-TYPE  7 80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2   18
  1Q GAIN WILD-TYPE    7   80
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              18                80
[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   4
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5               114 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                 4 
$`3Q GAIN MUTATED`
TCGA-4V-A9QJ TCGA-X7-A8M3 TCGA-ZB-A966 TCGA-ZB-A96L TCGA-ZC-AAA7 
       88.83         1.64        12.46         0.30        28.04 

$`3Q GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QL TCGA-4V-A9QM 
       13.48         9.96        34.52        89.23        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F 
       39.45        19.50        34.65        11.57        10.36        15.09 
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        49.22 
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         2.37 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       14.50        42.15       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE 
       52.54        48.92        37.61        97.41        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 
       26.20        12.69        11.93        12.72        84.23        13.05 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T 
       32.25        37.81       112.11        35.90        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        18.67 
TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 
       13.32        22.78        49.78        12.79         0.13         0.20 
TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       30.74        18.58        16.57         0.66        10.68        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H 
       43.43        42.81         0.23         0.16        32.35        37.48 
TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
        5.19        31.50         0.46         1.81        10.68         7.17 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       35.34         8.52        26.93        38.30        16.34        68.91 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.30              0.13 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            88.83            149.98 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           12.460            31.875 
[1] "0.3 - 88.8 (12.5)"  "0.1 - 150.0 (31.9)"
[1] "hr=" "19" 
D3V2, continuous
D3V3, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    3  2
  3Q GAIN WILD-TYPE 56 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    2
  3Q GAIN WILD-TYPE   56   60
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               3                56
  MALE                 2                60
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       0                         0     5
  3Q GAIN WILD-TYPE    13                         6    95
D3V4, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   5                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"
D3V5, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    0  5
  3Q GAIN WILD-TYPE  9 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0    5
  3Q GAIN WILD-TYPE    9   93
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               5                93
[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   4
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11               108 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                 4 
$`5P GAIN MUTATED`
TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4V-A9QS TCGA-5U-AB0D TCGA-X7-A8M3 TCGA-XM-A8RC 
       28.90        19.76        19.76        11.57         1.64        97.41 
TCGA-XM-A8RI TCGA-XM-AAZ1 TCGA-XU-A92Y TCGA-XU-A931 TCGA-XU-A936 
       12.72        13.05       114.67        52.90        21.14 

$`5P GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       38.50        45.07        21.70        16.60        14.07        11.24 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ 
       15.78        12.89        23.57        55.46        39.45        19.50 
TCGA-5K-AAAP TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 
       34.65        10.36        15.09        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        49.22        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         2.37        14.50        42.15       125.19 
TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       54.08        83.28        30.08        52.54        48.92        37.61 
TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RL 
       50.83         7.69        26.20        12.69        11.93        84.23 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T 
       32.25        37.81       112.11        35.90        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-A95F TCGA-YT-A95G 
       49.38       107.44        18.67        13.32        22.78        49.78 
TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 
       12.79         0.13         0.20        30.74        18.58        16.57 
TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D 
       12.46         0.66        10.68        60.33        43.43        42.81 
TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K 
        0.23         0.16        32.35        37.48         5.19        31.50 
TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
        0.30         0.46         1.81        10.68         7.17        35.34 
TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
        8.52        28.04        26.93        38.30        16.34        68.91 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             1.64              0.13 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           114.67            149.98 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            19.76             32.25 
[1] "1.6 - 114.7 (19.8)" "0.1 - 150.0 (32.2)"
[1] "hr=" "4.5"
D4V2, continuous
D4V3, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    8  3
  5P GAIN WILD-TYPE 51 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      8    3
  5P GAIN WILD-TYPE   51   59
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               8                51
  MALE                 3                59
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       0                         0    10
  5P GAIN WILD-TYPE    13                         6    90
D4V4, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  10                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"
D4V5, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    2  7
  5P GAIN WILD-TYPE  7 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2    7
  5P GAIN WILD-TYPE    7   91
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO               7                91
[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   4
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9               110 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                 4 
$`5Q GAIN MUTATED`
TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4V-A9QS TCGA-X7-A8M3 TCGA-XM-A8RC TCGA-XM-A8RI 
       28.90        19.76        19.76         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-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       38.50        45.07        21.70        16.60        14.07        11.24 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ 
       15.78        12.89        23.57        55.46        39.45        19.50 
TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 
       34.65        11.57        10.36        15.09        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        49.22        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         2.37        14.50        42.15 
TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      125.19        54.08        83.28        30.08        52.54        48.92 
TCGA-XM-A8RB TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH 
       37.61        50.83         7.69        26.20        12.69        11.93 
TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q 
       84.23        13.05        32.25        37.81       112.11        35.90 
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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       22.78        49.78        12.79         0.13         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       18.58        16.57        12.46         0.66        10.68        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H 
       43.43        42.81         0.23         0.16        32.35        37.48 
TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
        5.19        31.50         0.30         0.46         1.81        10.68 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
        7.17        35.34         8.52        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 
       16.34        68.91 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             1.64              0.13 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           114.67            149.98 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           21.140            31.875 
[1] "1.6 - 114.7 (21.1)" "0.1 - 150.0 (31.9)"
[1] "hr=" "4.8"
D5V2, continuous
D5V3, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    7  2
  5Q GAIN WILD-TYPE 52 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7    2
  5Q GAIN WILD-TYPE   52   60
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               7                52
  MALE                 2                60
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       0                         0     8
  5Q GAIN WILD-TYPE    13                         6    92
D5V4, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   8                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"
D5V5, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    1  6
  5Q GAIN WILD-TYPE  8 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1    6
  5Q GAIN WILD-TYPE    8   92
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO               6                92
[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   3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               16               103 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                3                 3 
$`7P GAIN MUTATED`
TCGA-3G-AB0T TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4X-A9FD TCGA-5U-AB0E TCGA-X7-A8M3 
       81.80        19.76        19.76        39.45        10.36         1.64 
TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RI TCGA-XM-AAZ1 TCGA-XU-A92X TCGA-XU-A92Y 
       97.41        50.83        12.72        13.05        77.03       114.67 
TCGA-XU-A930 TCGA-XU-A931 TCGA-ZB-A96F TCGA-ZB-A96I 
       82.65        52.90         0.16         5.19 

$`7P GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-A8YW 
       56.65        59.15        17.75        90.61        15.35        13.48 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       28.90        45.07        21.70        16.60        14.07        11.24 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-5G-A9ZZ TCGA-5K-AAAP 
       15.78        12.89        23.57        55.46        19.50        34.65 
TCGA-5U-AB0D TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 
       11.57        15.09        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        49.22        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         2.37        14.50        42.15       125.19        54.08 
TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE 
       83.28        30.08        52.54        48.92        37.61         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       26.20        12.69        11.93        84.23        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
      112.11        35.90        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        18.67 
TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 
       13.32        22.78        49.78        12.79         0.13         0.20 
TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A 
       30.74        18.58        16.57        12.46         0.66        10.68 
TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H 
       60.33        43.43        42.81         0.23        32.35        37.48 
TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       31.50         0.30         0.46         1.81        10.68         7.17 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
       35.34         8.52        28.04        26.93        38.30        16.34 
TCGA-ZL-A9V6 
       68.91 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.16              0.13 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           114.67            149.98 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           29.605            30.740 
[1] "0.2 - 114.7 (29.6)" "0.1 - 150.0 (30.7)"
[1] "hr=" "5.5"
D6V2, continuous
D6V3, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    8  8
  7P GAIN WILD-TYPE 51 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      8    8
  7P GAIN WILD-TYPE   51   54
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               8                51
  MALE                 8                54
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       1                         0    14
  7P GAIN WILD-TYPE    12                         6    86
D6V4, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  14                86
[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"
D6V5, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    1 13
  7P GAIN WILD-TYPE  8 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      1   13
  7P GAIN WILD-TYPE    8   85
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              13                85
[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   3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               16               103 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                3                 3 
$`7Q GAIN MUTATED`
TCGA-3G-AB0T TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4X-A9FD TCGA-5U-AB0E TCGA-X7-A8M3 
       81.80        19.76        19.76        39.45        10.36         1.64 
TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RI TCGA-XM-AAZ1 TCGA-XU-A92X TCGA-XU-A92Y 
       97.41        50.83        12.72        13.05        77.03       114.67 
TCGA-XU-A930 TCGA-XU-A931 TCGA-ZB-A96F TCGA-ZB-A96I 
       82.65        52.90         0.16         5.19 

$`7Q GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-A8YW 
       56.65        59.15        17.75        90.61        15.35        13.48 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       28.90        45.07        21.70        16.60        14.07        11.24 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-5G-A9ZZ TCGA-5K-AAAP 
       15.78        12.89        23.57        55.46        19.50        34.65 
TCGA-5U-AB0D TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 
       11.57        15.09        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        49.22        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         2.37        14.50        42.15       125.19        54.08 
TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE 
       83.28        30.08        52.54        48.92        37.61         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       26.20        12.69        11.93        84.23        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
      112.11        35.90        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        18.67 
TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 
       13.32        22.78        49.78        12.79         0.13         0.20 
TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A 
       30.74        18.58        16.57        12.46         0.66        10.68 
TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H 
       60.33        43.43        42.81         0.23        32.35        37.48 
TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       31.50         0.30         0.46         1.81        10.68         7.17 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
       35.34         8.52        28.04        26.93        38.30        16.34 
TCGA-ZL-A9V6 
       68.91 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.16              0.13 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           114.67            149.98 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           29.605            30.740 
[1] "0.2 - 114.7 (29.6)" "0.1 - 150.0 (30.7)"
[1] "hr=" "5.5"
D7V2, continuous
D7V3, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    8  8
  7Q GAIN WILD-TYPE 51 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      8    8
  7Q GAIN WILD-TYPE   51   54
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               8                51
  MALE                 8                54
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       1                         0    14
  7Q GAIN WILD-TYPE    12                         6    86
D7V4, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  14                86
[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"
D7V5, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    1 13
  7Q GAIN WILD-TYPE  8 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      1   13
  7Q GAIN WILD-TYPE    8   85
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              13                85
[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   4
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12               107 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                 4 
$`8P GAIN MUTATED`
TCGA-3G-AB0T TCGA-3S-A8YW TCGA-X7-A8M3 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-AAZ1 
       81.80        13.48         1.64        37.61        97.41        13.05 
TCGA-XU-A932 TCGA-XU-A936 TCGA-YT-A95G TCGA-ZB-A96F TCGA-ZB-A96V TCGA-ZC-AAA7 
       70.65        21.14        49.78         0.16         8.52        28.04 

$`8P GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-AAYX 
       56.65        59.15        17.75        90.61        15.35         9.96 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN 
       34.52        89.23        88.83        56.75        38.50        28.90 
TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW 
       45.07        19.76        19.76        21.70        16.60        14.07 
TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-4X-A9FD 
       11.24        15.78        12.89        23.57        55.46        39.45 
TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR 
       19.50        34.65        11.57        10.36        15.09        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        49.22        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         2.37        14.50 
TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
       42.15       125.19        54.08        83.28        30.08        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH 
       48.92        50.83         7.69        26.20        12.69        11.93 
TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q 
       12.72        84.23        32.25        37.81       112.11        35.90 
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        18.67 
TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       13.32        22.78        12.79         0.13         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       18.58        16.57        12.46         0.66        10.68        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I 
       43.43        42.81         0.23        32.35        37.48         5.19 
TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       31.50         0.30         0.46         1.81        10.68         7.17 
TCGA-ZB-A96R TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       35.34        26.93        38.30        16.34        68.91 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.16              0.13 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            97.41            149.98 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            24.59             31.50 
[1] "0.2 - 97.4 (24.6)"  "0.1 - 150.0 (31.5)"
[1] "hr=" "6.3"
D8V2, continuous
D8V3, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    4  8
  8P GAIN WILD-TYPE 55 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4    8
  8P GAIN WILD-TYPE   55   54
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               4                55
  MALE                 8                54
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       1                         1    10
  8P GAIN WILD-TYPE    12                         5    90
D8V4, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                  10                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"
D8V5, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    1 10
  8P GAIN WILD-TYPE  8 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   10
  8P GAIN WILD-TYPE    8   88
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              10                88
[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   4
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               12               107 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                 4 
$`8Q GAIN MUTATED`
TCGA-3G-AB0T TCGA-3S-A8YW TCGA-X7-A8M3 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-AAZ1 
       81.80        13.48         1.64        37.61        97.41        13.05 
TCGA-XU-A932 TCGA-XU-A936 TCGA-YT-A95G TCGA-ZB-A96F TCGA-ZB-A96V TCGA-ZC-AAA7 
       70.65        21.14        49.78         0.16         8.52        28.04 

$`8Q GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-AAYX 
       56.65        59.15        17.75        90.61        15.35         9.96 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN 
       34.52        89.23        88.83        56.75        38.50        28.90 
TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW 
       45.07        19.76        19.76        21.70        16.60        14.07 
TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-4X-A9FD 
       11.24        15.78        12.89        23.57        55.46        39.45 
TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR 
       19.50        34.65        11.57        10.36        15.09        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        49.22        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         2.37        14.50 
TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
       42.15       125.19        54.08        83.28        30.08        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH 
       48.92        50.83         7.69        26.20        12.69        11.93 
TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q 
       12.72        84.23        32.25        37.81       112.11        35.90 
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        18.67 
TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       13.32        22.78        12.79         0.13         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       18.58        16.57        12.46         0.66        10.68        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I 
       43.43        42.81         0.23        32.35        37.48         5.19 
TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       31.50         0.30         0.46         1.81        10.68         7.17 
TCGA-ZB-A96R TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       35.34        26.93        38.30        16.34        68.91 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.16              0.13 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            97.41            149.98 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            24.59             31.50 
[1] "0.2 - 97.4 (24.6)"  "0.1 - 150.0 (31.5)"
[1] "hr=" "6.3"
D9V2, continuous
D9V3, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    4  8
  8Q GAIN WILD-TYPE 55 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      4    8
  8Q GAIN WILD-TYPE   55   54
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               4                55
  MALE                 8                54
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       1                         1    10
  8Q GAIN WILD-TYPE    12                         5    90
D9V4, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                  10                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"
D9V5, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    1 10
  8Q GAIN WILD-TYPE  8 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   10
  8Q GAIN WILD-TYPE    8   88
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              10                88
[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   4
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               11               108 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                 4 
$`9P GAIN MUTATED`
TCGA-3G-AB0T TCGA-4V-A9QR TCGA-4V-A9QS TCGA-XM-AAZ1 TCGA-XU-A92R TCGA-XU-A92X 
       81.80        19.76        19.76        13.05        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         0.16 

$`9P GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-A8YW 
       56.65        59.15        17.75        90.61        15.35        13.48 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       28.90        45.07        21.70        16.60        14.07        11.24 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ 
       15.78        12.89        23.57        55.46        39.45        19.50 
TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 
       34.65        11.57        10.36        15.09        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        49.22        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         2.37        14.50        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
        1.64       125.19        54.08        83.28        30.08        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF 
       48.92        37.61        97.41        50.83         7.69        26.20 
TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       12.69        11.93        12.72        84.23        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W 
      112.11        35.90        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-A95F 
       50.53        49.38       107.44        18.67        13.32        22.78 
TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       49.78        12.79         0.13         0.20        30.74        18.58 
TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C 
       16.57        12.46         0.66        10.68        60.33        43.43 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K 
       42.81         0.23        32.35        37.48         5.19        31.50 
TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
        0.30         0.46         1.81        10.68         7.17        35.34 
TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
        8.52        28.04        26.93        38.30        16.34        68.91 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.16              0.13 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           123.68            149.98 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            70.65             29.85 
[1] "0.2 - 123.7 (70.7)" "0.1 - 150.0 (29.9)"
[1] "hr=" "2.9"
D10V2, continuous
D10V3, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    5  6
  9P GAIN WILD-TYPE 54 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      5    6
  9P GAIN WILD-TYPE   54   56
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               5                54
  MALE                 6                56
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       4                         0     7
  9P GAIN WILD-TYPE     9                         6    93
D10V4, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   4                 9
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   7                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    0 10
  9P GAIN WILD-TYPE  9 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   10
  9P GAIN WILD-TYPE    9   88
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              10                88
[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   4
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               11               108 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                 4 
$`9Q GAIN MUTATED`
TCGA-3G-AB0T TCGA-4V-A9QR TCGA-4V-A9QS TCGA-XM-AAZ1 TCGA-XU-A92R TCGA-XU-A92X 
       81.80        19.76        19.76        13.05        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         0.16 

$`9Q GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-A8YW 
       56.65        59.15        17.75        90.61        15.35        13.48 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       28.90        45.07        21.70        16.60        14.07        11.24 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ 
       15.78        12.89        23.57        55.46        39.45        19.50 
TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 
       34.65        11.57        10.36        15.09        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        49.22        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         2.37        14.50        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
        1.64       125.19        54.08        83.28        30.08        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF 
       48.92        37.61        97.41        50.83         7.69        26.20 
TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       12.69        11.93        12.72        84.23        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W 
      112.11        35.90        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-A95F 
       50.53        49.38       107.44        18.67        13.32        22.78 
TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       49.78        12.79         0.13         0.20        30.74        18.58 
TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C 
       16.57        12.46         0.66        10.68        60.33        43.43 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K 
       42.81         0.23        32.35        37.48         5.19        31.50 
TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
        0.30         0.46         1.81        10.68         7.17        35.34 
TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
        8.52        28.04        26.93        38.30        16.34        68.91 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.16              0.13 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           123.68            149.98 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            70.65             29.85 
[1] "0.2 - 123.7 (70.7)" "0.1 - 150.0 (29.9)"
[1] "hr=" "2.9"
D11V2, continuous
D11V3, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    5  6
  9Q GAIN WILD-TYPE 54 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      5    6
  9Q GAIN WILD-TYPE   54   56
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               5                54
  MALE                 6                56
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       4                         0     7
  9Q GAIN WILD-TYPE     9                         6    93
D11V4, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   4                 9
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   7                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    0 10
  9Q GAIN WILD-TYPE  9 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   10
  9Q GAIN WILD-TYPE    9   88
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              10                88
[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   5
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                115 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 1                  5 
$`12P GAIN MUTATED`
TCGA-3S-A8YW TCGA-XM-A8RC TCGA-XU-A936 TCGA-ZC-AAA7 
       13.48        97.41        21.14        28.04 

$`12P GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F 
       39.45        19.50        34.65        11.57        10.36        15.09 
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        49.22 
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         2.37 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 
       14.50        42.15         1.64       125.19        54.08        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RD TCGA-XM-A8RE 
       30.08        52.54        48.92        37.61        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 
       26.20        12.69        11.93        12.72        84.23        13.05 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T 
       32.25        37.81       112.11        35.90        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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       22.78        49.78        12.79         0.13         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       18.58        16.57        12.46         0.66        10.68        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H 
       43.43        42.81         0.23         0.16        32.35        37.48 
TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
        5.19        31.50         0.30         0.46         1.81        10.68 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
        7.17        35.34         8.52        26.93        38.30        16.34 
TCGA-ZL-A9V6 
       68.91 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             13.48               0.13 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             97.41             149.98 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             24.59              31.50 
[1] "13.5 - 97.4 (24.6)" "0.1 - 150.0 (31.5)"
[1] "hr=" "6.2"
D12V2, continuous
D12V3, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    1  3
  12P GAIN WILD-TYPE 58 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1    3
  12P GAIN WILD-TYPE   58   59
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                1                 58
  MALE                  3                 59
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       0                         0     4
  12P GAIN WILD-TYPE    13                         6    96
D12V4, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    4                 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"
D12V5, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    1  3
  12P GAIN WILD-TYPE  8 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1    3
  12P GAIN WILD-TYPE    8   95
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO                3                 95
[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   5
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                115 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 1                  5 
$`12Q GAIN MUTATED`
TCGA-3S-A8YW TCGA-XM-A8RC TCGA-XU-A936 TCGA-ZC-AAA7 
       13.48        97.41        21.14        28.04 

$`12Q GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F 
       39.45        19.50        34.65        11.57        10.36        15.09 
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        49.22 
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         2.37 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 
       14.50        42.15         1.64       125.19        54.08        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RD TCGA-XM-A8RE 
       30.08        52.54        48.92        37.61        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 
       26.20        12.69        11.93        12.72        84.23        13.05 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T 
       32.25        37.81       112.11        35.90        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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       22.78        49.78        12.79         0.13         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       18.58        16.57        12.46         0.66        10.68        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H 
       43.43        42.81         0.23         0.16        32.35        37.48 
TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
        5.19        31.50         0.30         0.46         1.81        10.68 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
        7.17        35.34         8.52        26.93        38.30        16.34 
TCGA-ZL-A9V6 
       68.91 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             13.48               0.13 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             97.41             149.98 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             24.59              31.50 
[1] "13.5 - 97.4 (24.6)" "0.1 - 150.0 (31.5)"
[1] "hr=" "6.2"
D13V2, continuous
D13V3, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    1  3
  12Q GAIN WILD-TYPE 58 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    3
  12Q GAIN WILD-TYPE   58   59
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                1                 58
  MALE                  3                 59
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       0                         0     4
  12Q GAIN WILD-TYPE    13                         6    96
D13V4, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    4                 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"
D13V5, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    1  3
  12Q GAIN WILD-TYPE  8 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    3
  12Q GAIN WILD-TYPE    8   95
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO                3                 95
[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   4
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                13                106 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                  4 
$`14Q GAIN MUTATED`
TCGA-3G-AB0T TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4X-A9FD TCGA-X7-A8M3 TCGA-XM-A8RC 
       81.80        19.76        19.76        39.45         1.64        97.41 
TCGA-XM-A8RI TCGA-XM-AAZ1 TCGA-XU-A92X TCGA-XU-A931 TCGA-XU-AAXW TCGA-XU-AAXX 
       12.72        13.05        77.03        52.90       123.68        89.46 
TCGA-ZB-A96F 
        0.16 

$`14Q GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-A8YW 
       56.65        59.15        17.75        90.61        15.35        13.48 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       28.90        45.07        21.70        16.60        14.07        11.24 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-5G-A9ZZ TCGA-5K-AAAP 
       15.78        12.89        23.57        55.46        19.50        34.65 
TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 
       11.57        10.36        15.09        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        49.22        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         2.37        14.50        42.15       125.19 
TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       54.08        83.28        30.08        52.54        48.92        37.61 
TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RL 
       50.83         7.69        26.20        12.69        11.93        84.23 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T 
       32.25        37.81       112.11        35.90        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-A95F TCGA-YT-A95G TCGA-YT-A95H 
      107.44        18.67        13.32        22.78        49.78        12.79 
TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 
        0.13         0.20        30.74        18.58        16.57        12.46 
TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E 
        0.66        10.68        60.33        43.43        42.81         0.23 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M 
       32.35        37.48         5.19        31.50         0.30         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
        1.81        10.68         7.17        35.34         8.52        28.04 
TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       26.93        38.30        16.34        68.91 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.16               0.13 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            123.68             149.98 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             39.45              30.41 
[1] "0.2 - 123.7 (39.5)" "0.1 - 150.0 (30.4)"
[1] "hr=" "2.9"
D14V2, continuous
D14V3, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    7  6
  14Q GAIN WILD-TYPE 52 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      7    6
  14Q GAIN WILD-TYPE   52   56
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                7                 52
  MALE                  6                 56
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       2                         0    10
  14Q GAIN WILD-TYPE    11                         6    90
D14V4, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    2                 11
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                   10                 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"
D14V5, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    0 10
  14Q GAIN WILD-TYPE  9 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   10
  14Q GAIN WILD-TYPE    9   88
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               10                 88
[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   4
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                12                107 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                  4 
$`15Q GAIN MUTATED`
TCGA-3G-AB0T TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-5U-AB0E TCGA-XM-A8RC 
       81.80        45.07        19.76        19.76        10.36        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         0.16 

$`15Q GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-A8YW 
       56.65        59.15        17.75        90.61        15.35        13.48 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 
       28.90        21.70        16.60        14.07        11.24        15.78 
TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP 
       12.89        23.57        55.46        39.45        19.50        34.65 
TCGA-5U-AB0D TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 
       11.57        15.09        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        49.22        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         2.37        14.50        42.15         1.64       125.19 
TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       54.08        83.28        30.08        52.54        48.92        37.61 
TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
       50.83         7.69        12.69        11.93        12.72        84.23 
TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R 
       13.05        32.25        37.81       112.11        35.90        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-A95F TCGA-YT-A95G 
       49.38       107.44        18.67        13.32        22.78        49.78 
TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 
       12.79         0.13         0.20        30.74        18.58        16.57 
TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D 
       12.46         0.66        10.68        60.33        43.43        42.81 
TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L 
        0.23        32.35        37.48         5.19        31.50         0.30 
TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V 
        0.46         1.81        10.68         7.17        35.34         8.52 
TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       28.04        26.93        38.30        16.34        68.91 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.16               0.13 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            114.67             149.98 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            35.635             30.740 
[1] "0.2 - 114.7 (35.6)" "0.1 - 150.0 (30.7)"
[1] "hr=" "3.5"
D15V2, continuous
D15V3, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    6  6
  15Q GAIN WILD-TYPE 53 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      6    6
  15Q GAIN WILD-TYPE   53   56
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                6                 53
  MALE                  6                 56
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       1                         0    11
  15Q GAIN WILD-TYPE    12                         6    89
D15V4, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                   11                 89
[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"
D15V5, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    1 11
  15Q GAIN WILD-TYPE  8 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   11
  15Q GAIN WILD-TYPE    8   87
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               11                 87
[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   6
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                112 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 0                  6 
$`17Q GAIN MUTATED`
TCGA-4V-A9QJ TCGA-5G-A9ZZ TCGA-XM-A8RC TCGA-XM-A8RG TCGA-XU-A933 TCGA-XU-A936 
       88.83        19.50        97.41        12.69        58.82        21.14 
TCGA-ZB-A962 
        0.20 

$`17Q GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QL TCGA-4V-A9QM 
       13.48         9.96        34.52        89.23        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR 
       39.45        34.65        11.57        10.36        15.09        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        49.22        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         2.37        14.50 
TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       42.15         1.64       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF 
       52.54        48.92        37.61        50.83         7.69        26.20 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       11.93        12.72        84.23        13.05        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
      112.11        35.90        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-A95F TCGA-YT-A95G TCGA-YT-A95H 
      107.44        18.67        13.32        22.78        49.78        12.79 
TCGA-ZB-A961 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 
        0.13        30.74        18.58        16.57        12.46         0.66 
TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F 
       10.68        60.33        43.43        42.81         0.23         0.16 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M 
       32.35        37.48         5.19        31.50         0.30         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
        1.81        10.68         7.17        35.34         8.52        28.04 
TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       26.93        38.30        16.34        68.91 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.20               0.13 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             97.41             149.98 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             21.14              31.12 
[1] "0.2 - 97.4 (21.1)"  "0.1 - 150.0 (31.1)"
[1] "hr="     "7.5e+07"
D16V2, continuous
D16V3, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    3  4
  17Q GAIN WILD-TYPE 56 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3    4
  17Q GAIN WILD-TYPE   56   58
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                3                 56
  MALE                  4                 58
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       1                         0     6
  17Q GAIN WILD-TYPE    12                         6    94
D16V4, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    6                 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"
D16V5, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    0  7
  17Q GAIN WILD-TYPE  9 91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0    7
  17Q GAIN WILD-TYPE    9   91
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                7                 91
[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   6
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                116 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                  6 
$`18P GAIN MUTATED`
TCGA-3S-A8YW TCGA-XU-A936 TCGA-ZB-A96F 
       13.48        21.14         0.16 

$`18P GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F 
       39.45        19.50        34.65        11.57        10.36        15.09 
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        49.22 
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         2.37 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 
       14.50        42.15         1.64       125.19        54.08        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD 
       30.08        52.54        48.92        37.61        97.41        50.83 
TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
        7.69        26.20        12.69        11.93        12.72        84.23 
TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R 
       13.05        32.25        37.81       112.11        35.90        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        18.67 
TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 
       13.32        22.78        49.78        12.79         0.13         0.20 
TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A 
       30.74        18.58        16.57        12.46         0.66        10.68 
TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H 
       60.33        43.43        42.81         0.23        32.35        37.48 
TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
        5.19        31.50         0.30         0.46         1.81        10.68 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
        7.17        35.34         8.52        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 
       16.34        68.91 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.16               0.13 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             21.14             149.98 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            13.480             31.875 
[1] "0.2 - 21.1 (13.5)"  "0.1 - 150.0 (31.9)"
[1] "hr="     "3400000"
D17V2, continuous
D17V3, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    1  2
  18P GAIN WILD-TYPE 58 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    2
  18P GAIN WILD-TYPE   58   60
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                1                 58
  MALE                  2                 60
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       0                         0     3
  18P GAIN WILD-TYPE    13                         6    97
D17V4, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                 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"
D17V5, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    1  2
  18P GAIN WILD-TYPE  8 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    2
  18P GAIN WILD-TYPE    8   96
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO                2                 96
[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   6
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                116 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                  6 
$`18Q GAIN MUTATED`
TCGA-3S-A8YW TCGA-XU-A936 TCGA-ZB-A96F 
       13.48        21.14         0.16 

$`18Q GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F 
       39.45        19.50        34.65        11.57        10.36        15.09 
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        49.22 
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         2.37 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 
       14.50        42.15         1.64       125.19        54.08        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD 
       30.08        52.54        48.92        37.61        97.41        50.83 
TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
        7.69        26.20        12.69        11.93        12.72        84.23 
TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R 
       13.05        32.25        37.81       112.11        35.90        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        18.67 
TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 
       13.32        22.78        49.78        12.79         0.13         0.20 
TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A 
       30.74        18.58        16.57        12.46         0.66        10.68 
TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H 
       60.33        43.43        42.81         0.23        32.35        37.48 
TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
        5.19        31.50         0.30         0.46         1.81        10.68 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
        7.17        35.34         8.52        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 
       16.34        68.91 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.16               0.13 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             21.14             149.98 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            13.480             31.875 
[1] "0.2 - 21.1 (13.5)"  "0.1 - 150.0 (31.9)"
[1] "hr="     "3400000"
D18V2, continuous
D18V3, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    1  2
  18Q GAIN WILD-TYPE 58 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    2
  18Q GAIN WILD-TYPE   58   60
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                 58
  MALE                  2                 60
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       0                         0     3
  18Q GAIN WILD-TYPE    13                         6    97
D18V4, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                 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"
D18V5, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    1  2
  18Q GAIN WILD-TYPE  8 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    2
  18Q GAIN WILD-TYPE    8   96
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO                2                 96
[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   6
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                116 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 0                  6 
$`19P GAIN MUTATED`
TCGA-4V-A9QR TCGA-X7-A8M3 TCGA-XU-A930 
       19.76         1.64        82.65 

$`19P GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       38.50        28.90        45.07        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F 
       39.45        19.50        34.65        11.57        10.36        15.09 
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        49.22 
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         2.37 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       14.50        42.15       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE 
       52.54        48.92        37.61        97.41        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 
       26.20        12.69        11.93        12.72        84.23        13.05 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T 
       32.25        37.81       112.11        35.90        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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       22.78        49.78        12.79         0.13         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       18.58        16.57        12.46         0.66        10.68        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H 
       43.43        42.81         0.23         0.16        32.35        37.48 
TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
        5.19        31.50         0.30         0.46         1.81        10.68 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
        7.17        35.34         8.52        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 
       16.34        68.91 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              1.64               0.13 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             82.65             149.98 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             19.76              31.12 
[1] "1.6 - 82.7 (19.8)"  "0.1 - 150.0 (31.1)"
[1] "hr="     "2.6e+07"
D19V2, continuous
D19V3, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    2  1
  19P GAIN WILD-TYPE 57 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2    1
  19P GAIN WILD-TYPE   57   61
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                2                 57
  MALE                  1                 61
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       0                         0     3
  19P GAIN WILD-TYPE    13                         6    97
D19V4, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                 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"
D19V5, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    0  3
  19P GAIN WILD-TYPE  9 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    3
  19P GAIN WILD-TYPE    9   95
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                3                 95
[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   6
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                116 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                  6 
$`19Q GAIN MUTATED`
TCGA-4V-A9QR TCGA-X7-A8M3 TCGA-XU-A930 
       19.76         1.64        82.65 

$`19Q GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       38.50        28.90        45.07        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F 
       39.45        19.50        34.65        11.57        10.36        15.09 
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        49.22 
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         2.37 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       14.50        42.15       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE 
       52.54        48.92        37.61        97.41        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 
       26.20        12.69        11.93        12.72        84.23        13.05 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T 
       32.25        37.81       112.11        35.90        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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       22.78        49.78        12.79         0.13         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       18.58        16.57        12.46         0.66        10.68        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H 
       43.43        42.81         0.23         0.16        32.35        37.48 
TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
        5.19        31.50         0.30         0.46         1.81        10.68 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
        7.17        35.34         8.52        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 
       16.34        68.91 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              1.64               0.13 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             82.65             149.98 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             19.76              31.12 
[1] "1.6 - 82.7 (19.8)"  "0.1 - 150.0 (31.1)"
[1] "hr="     "2.6e+07"
D20V2, continuous
D20V3, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    2  1
  19Q GAIN WILD-TYPE 57 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    1
  19Q GAIN WILD-TYPE   57   61
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                2                 57
  MALE                  1                 61
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       0                         0     3
  19Q GAIN WILD-TYPE    13                         6    97
D20V4, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                 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"
D20V5, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    0  3
  19Q GAIN WILD-TYPE  9 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0    3
  19Q GAIN WILD-TYPE    9   95
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                3                 95
[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   5
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                10                109 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 1                  5 
$`20P GAIN MUTATED`
TCGA-4V-A9QJ TCGA-4V-A9QR TCGA-5U-AB0D TCGA-5U-AB0E TCGA-X7-A8M3 TCGA-XM-A8RC 
       88.83        19.76        11.57        10.36         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-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QL TCGA-4V-A9QM 
       13.48         9.96        34.52        89.23        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW 
       28.90        45.07        19.76        21.70        16.60        14.07 
TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-4X-A9FD 
       11.24        15.78        12.89        23.57        55.46        39.45 
TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 
       19.50        34.65        15.09        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        49.22        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         2.37        14.50        42.15       125.19 
TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       54.08        83.28        30.08        52.54        48.92        37.61 
TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI 
       50.83         7.69        26.20        12.69        11.93        12.72 
TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q 
       84.23        13.05        32.25        37.81       112.11        35.90 
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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       22.78        49.78        12.79         0.13         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       18.58        16.57        12.46         0.66        10.68        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H 
       43.43        42.81         0.23         0.16        32.35        37.48 
TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
        5.19        31.50         0.30         0.46         1.81        10.68 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
        7.17        35.34         8.52        26.93        38.30        16.34 
TCGA-ZL-A9V6 
       68.91 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              1.64               0.13 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             97.41             149.98 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             24.59              31.50 
[1] "1.6 - 97.4 (24.6)"  "0.1 - 150.0 (31.5)"
[1] "hr=" "2.4"
D21V2, continuous
D21V3, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    5  5
  20P GAIN WILD-TYPE 54 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5    5
  20P GAIN WILD-TYPE   54   57
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                5                 54
  MALE                  5                 57
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       2                         0     8
  20P GAIN WILD-TYPE    11                         6    92
D21V4, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    2                 11
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    8                 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"
D21V5, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    2  8
  20P GAIN WILD-TYPE  7 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2    8
  20P GAIN WILD-TYPE    7   90
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO                8                 90
[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   5
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                109 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 1                  5 
$`20Q GAIN MUTATED`
TCGA-4V-A9QJ TCGA-4V-A9QR TCGA-5U-AB0D TCGA-5U-AB0E TCGA-X7-A8M3 TCGA-XM-A8RC 
       88.83        19.76        11.57        10.36         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-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QL TCGA-4V-A9QM 
       13.48         9.96        34.52        89.23        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW 
       28.90        45.07        19.76        21.70        16.60        14.07 
TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-4X-A9FD 
       11.24        15.78        12.89        23.57        55.46        39.45 
TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 
       19.50        34.65        15.09        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        49.22        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         2.37        14.50        42.15       125.19 
TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       54.08        83.28        30.08        52.54        48.92        37.61 
TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI 
       50.83         7.69        26.20        12.69        11.93        12.72 
TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q 
       84.23        13.05        32.25        37.81       112.11        35.90 
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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       22.78        49.78        12.79         0.13         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       18.58        16.57        12.46         0.66        10.68        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H 
       43.43        42.81         0.23         0.16        32.35        37.48 
TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
        5.19        31.50         0.30         0.46         1.81        10.68 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
        7.17        35.34         8.52        26.93        38.30        16.34 
TCGA-ZL-A9V6 
       68.91 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              1.64               0.13 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             97.41             149.98 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             24.59              31.50 
[1] "1.6 - 97.4 (24.6)"  "0.1 - 150.0 (31.5)"
[1] "hr=" "2.4"
D22V2, continuous
D22V3, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    5  5
  20Q GAIN WILD-TYPE 54 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5    5
  20Q GAIN WILD-TYPE   54   57
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                5                 54
  MALE                  5                 57
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       2                         0     8
  20Q GAIN WILD-TYPE    11                         6    92
D22V4, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    2                 11
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    8                 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"
D22V5, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    2  8
  20Q GAIN WILD-TYPE  7 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2    8
  20Q GAIN WILD-TYPE    7   90
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO                8                 90
[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   6
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                116 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 0                  6 
$`21Q GAIN MUTATED`
TCGA-X7-A8M3 TCGA-XU-A936 TCGA-ZB-A969 
        1.64        21.14         0.66 

$`21Q GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT 
       38.50        28.90        45.07        19.76        19.76        21.70 
TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB 
       16.60        14.07        11.24        15.78        12.89        23.57 
TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E 
       55.46        39.45        19.50        34.65        11.57        10.36 
TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB 
       15.09        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 
       49.22        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-A8M8 
        2.37        14.50        42.15       125.19        54.08        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD 
       30.08        52.54        48.92        37.61        97.41        50.83 
TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
        7.69        26.20        12.69        11.93        12.72        84.23 
TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R 
       13.05        32.25        37.81       112.11        35.90        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        18.67 
TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 
       13.32        22.78        49.78        12.79         0.13         0.20 
TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A96A TCGA-ZB-A96B 
       30.74        18.58        16.57        12.46        10.68        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H 
       43.43        42.81         0.23         0.16        32.35        37.48 
TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
        5.19        31.50         0.30         0.46         1.81        10.68 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
        7.17        35.34         8.52        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 
       16.34        68.91 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.66               0.13 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             21.14             149.98 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             1.640             31.875 
[1] "0.7 - 21.1 (1.6)"   "0.1 - 150.0 (31.9)"
[1] "hr="     "3300000"
D23V2, continuous
D23V3, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    3  0
  21Q GAIN WILD-TYPE 56 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    0
  21Q GAIN WILD-TYPE   56   62
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                3                 56
  MALE                  0                 62
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       0                         0     3
  21Q GAIN WILD-TYPE    13                         6    97
D23V4, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                 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"
D23V5, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    0  3
  21Q GAIN WILD-TYPE  9 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0    3
  21Q GAIN WILD-TYPE    9   95
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                3                 95
[1] 2 2
[1] FALSE

Clustering(24) Variable = 22Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED     5   0
  22Q GAIN WILD-TYPE 108   6
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                114 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 0                  6 
$`22Q GAIN MUTATED`
TCGA-4V-A9QR TCGA-4X-A9FD TCGA-X7-A8M3 TCGA-XU-A92X TCGA-ZB-A969 
       19.76        39.45         1.64        77.03         0.66 

$`22Q GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       38.50        28.90        45.07        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR 
       19.50        34.65        11.57        10.36        15.09        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        49.22        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         2.37        14.50 
TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
       42.15       125.19        54.08        83.28        30.08        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF 
       48.92        37.61        97.41        50.83         7.69        26.20 
TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 
       12.69        11.93        12.72        84.23        13.05        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U 
       37.81       112.11        35.90        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-A95F 
       50.53        49.38       107.44        18.67        13.32        22.78 
TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       49.78        12.79         0.13         0.20        30.74        18.58 
TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D 
       16.57        12.46        10.68        60.33        43.43        42.81 
TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K 
        0.23         0.16        32.35        37.48         5.19        31.50 
TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
        0.30         0.46         1.81        10.68         7.17        35.34 
TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
        8.52        28.04        26.93        38.30        16.34        68.91 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.66               0.13 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             77.03             149.98 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             19.76              31.12 
[1] "0.7 - 77.0 (19.8)"  "0.1 - 150.0 (31.1)"
[1] "hr="     "2.5e+07"
D24V2, continuous
D24V3, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    4  1
  22Q GAIN WILD-TYPE 55 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4    1
  22Q GAIN WILD-TYPE   55   61
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                4                 55
  MALE                  1                 61
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       1                         0     4
  22Q GAIN WILD-TYPE    12                         6    96
D24V4, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    4                 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"
D24V5, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    0  5
  22Q GAIN WILD-TYPE  9 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    5
  22Q GAIN WILD-TYPE    9   93
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO                5                 93
[1] 2 2
[1] FALSE

Clustering(25) Variable = XP GAIN MUTATION ANALYSIS
D25V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED     3   0
  XP GAIN WILD-TYPE 110   6
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                3               116 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                0                 6 
$`XP GAIN MUTATED`
TCGA-4V-A9QR TCGA-X7-A8M3 TCGA-ZB-A96I 
       19.76         1.64         5.19 

$`XP GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       38.50        28.90        45.07        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F 
       39.45        19.50        34.65        11.57        10.36        15.09 
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        49.22 
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         2.37 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       14.50        42.15       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE 
       52.54        48.92        37.61        97.41        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 
       26.20        12.69        11.93        12.72        84.23        13.05 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T 
       32.25        37.81       112.11        35.90        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        18.67 
TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 
       13.32        22.78        49.78        12.79         0.13         0.20 
TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A 
       30.74        18.58        16.57        12.46         0.66        10.68 
TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G 
       60.33        43.43        42.81         0.23         0.16        32.35 
TCGA-ZB-A96H TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
       37.48        31.50         0.30         0.46         1.81        10.68 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
        7.17        35.34         8.52        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 
       16.34        68.91 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             1.64              0.13 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            19.76            149.98 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            5.190            31.875 
[1] "1.6 - 19.8 (5.2)"   "0.1 - 150.0 (31.9)"
[1] "hr="     "3400000"
D25V2, continuous
D25V3, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    3  0
  XP GAIN WILD-TYPE 56 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      3    0
  XP GAIN WILD-TYPE   56   62
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE               3                56
  MALE                 0                62
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       0                         0     3
  XP GAIN WILD-TYPE    13                         6    97
D25V4, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   3                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"
D25V5, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    0  3
  XP GAIN WILD-TYPE  9 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0    3
  XP GAIN WILD-TYPE    9   95
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               3                95
[1] 2 2
[1] FALSE

Clustering(26) Variable = XQ GAIN MUTATION ANALYSIS
D26V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED     4   1
  XQ GAIN WILD-TYPE 109   5
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                5               114 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                 5 
$`XQ GAIN MUTATED`
TCGA-3G-AB0T TCGA-4V-A9QR TCGA-X7-A8M3 TCGA-ZB-A96F TCGA-ZB-A96I 
       81.80        19.76         1.64         0.16         5.19 

$`XQ GAIN WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-A8YW 
       56.65        59.15        17.75        90.61        15.35        13.48 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW 
       28.90        45.07        19.76        21.70        16.60        14.07 
TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-4X-A9FD 
       11.24        15.78        12.89        23.57        55.46        39.45 
TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR 
       19.50        34.65        11.57        10.36        15.09        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        49.22        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         2.37        14.50 
TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
       42.15       125.19        54.08        83.28        30.08        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF 
       48.92        37.61        97.41        50.83         7.69        26.20 
TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 
       12.69        11.93        12.72        84.23        13.05        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U 
       37.81       112.11        35.90        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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       22.78        49.78        12.79         0.13         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       18.58        16.57        12.46         0.66        10.68        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96K 
       43.43        42.81         0.23        32.35        37.48        31.50 
TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
        0.30         0.46         1.81        10.68         7.17        35.34 
TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
        8.52        28.04        26.93        38.30        16.34        68.91 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.16              0.13 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            81.80            149.98 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            5.190            31.875 
[1] "0.2 - 81.8 (5.2)"   "0.1 - 150.0 (31.9)"
[1] "hr=" "8.4"
D26V2, continuous
D26V3, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    3  2
  XQ GAIN WILD-TYPE 56 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3    2
  XQ GAIN WILD-TYPE   56   60
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               3                56
  MALE                 2                60
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       0                         0     5
  XQ GAIN WILD-TYPE    13                         6    95
D26V4, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   5                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"
D26V5, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    0  5
  XQ GAIN WILD-TYPE  9 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    5
  XQ GAIN WILD-TYPE    9   93
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               5                93
[1] 2 2
[1] FALSE

Clustering(27) Variable = 1P LOSS MUTATION ANALYSIS
D27V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED     4   0
  1P LOSS WILD-TYPE 109   6
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4               115 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                0                 6 
$`1P LOSS MUTATED`
TCGA-4V-A9QN TCGA-4X-A9FD TCGA-XU-A930 TCGA-XU-A936 
       28.90        39.45        82.65        21.14 

$`1P LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       38.50        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR 
       19.50        34.65        11.57        10.36        15.09        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        49.22        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         2.37        14.50 
TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       42.15         1.64       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE 
       52.54        48.92        37.61        97.41        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 
       26.20        12.69        11.93        12.72        84.23        13.05 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T 
       32.25        37.81       112.11        35.90        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-A95F 
       50.53        49.38       107.44        18.67        13.32        22.78 
TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       49.78        12.79         0.13         0.20        30.74        18.58 
TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C 
       16.57        12.46         0.66        10.68        60.33        43.43 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I 
       42.81         0.23         0.16        32.35        37.48         5.19 
TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       31.50         0.30         0.46         1.81        10.68         7.17 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
       35.34         8.52        28.04        26.93        38.30        16.34 
TCGA-ZL-A9V6 
       68.91 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            21.14              0.13 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            82.65            149.98 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           34.175            30.740 
[1] "21.1 - 82.7 (34.2)" "0.1 - 150.0 (30.7)"
[1] "hr="     "2.6e+07"
D27V2, continuous
D27V3, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    3  1
  1P LOSS WILD-TYPE 56 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    1
  1P LOSS WILD-TYPE   56   61
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               3                56
  MALE                 1                61
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       0                         0     4
  1P LOSS WILD-TYPE    13                         6    96
D27V4, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   4                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"
D27V5, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  3
  1P LOSS WILD-TYPE  8 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    3
  1P LOSS WILD-TYPE    8   95
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO               3                95
[1] 2 2
[1] FALSE

Clustering(28) Variable = 3P LOSS MUTATION ANALYSIS
D28V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    11   1
  3P LOSS WILD-TYPE 102   5
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               12               107 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                 5 
$`3P LOSS MUTATED`
TCGA-3G-AB14 TCGA-3S-A8YW TCGA-4V-A9QN TCGA-4X-A9FD TCGA-5U-AB0E TCGA-XM-A8RC 
       17.75        13.48        28.90        39.45        10.36        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         5.19        26.93 

$`3P LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-AAYX 
       56.65        59.15        81.80        90.61        15.35         9.96 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ 
       34.52        89.23        88.83        56.75        38.50        45.07 
TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       19.76        19.76        21.70        16.60        14.07        11.24 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-5G-A9ZZ TCGA-5K-AAAP 
       15.78        12.89        23.57        55.46        19.50        34.65 
TCGA-5U-AB0D TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 
       11.57        15.09        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        49.22        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         2.37        14.50        42.15         1.64       125.19 
TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       54.08        83.28        30.08        52.54        48.92        37.61 
TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI 
       50.83         7.69        26.20        12.69        11.93        12.72 
TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q 
       84.23        13.05        32.25        37.81       112.11        35.90 
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        18.67 
TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       13.32        22.78        12.79         0.13         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C 
       18.58        16.57         0.66        10.68        60.33        43.43 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96K 
       42.81         0.23         0.16        32.35        37.48        31.50 
TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
        0.30         0.46         1.81        10.68         7.17        35.34 
TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
        8.52        28.04        38.30        16.34        68.91 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             5.19              0.13 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            97.41            149.98 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           27.915            31.500 
[1] "5.2 - 97.4 (27.9)"  "0.1 - 150.0 (31.5)"
[1] "hr=" "2.2"
D28V2, continuous
D28V3, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    5  7
  3P LOSS WILD-TYPE 54 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5    7
  3P LOSS WILD-TYPE   54   55
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               5                54
  MALE                 7                55
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       1                         0    11
  3P LOSS WILD-TYPE    12                         6    89
D28V4, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  11                89
[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"
D28V5, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    4  7
  3P LOSS WILD-TYPE  5 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4    7
  3P LOSS WILD-TYPE    5   91
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO               7                91
[1] 2 2
[1] FALSE

Clustering(29) Variable = 3Q LOSS MUTATION ANALYSIS
D29V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     7   0
  3Q LOSS WILD-TYPE 106   6
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                7               112 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                0                 6 
$`3Q LOSS MUTATED`
TCGA-3S-A8YW TCGA-5U-AB0E TCGA-XM-A8RC TCGA-XU-A92X TCGA-XU-A930 TCGA-YT-A95G 
       13.48        10.36        97.41        77.03        82.65        49.78 
TCGA-ZC-AAAA 
       26.93 

$`3Q LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0F TCGA-5V-A9RR 
       39.45        19.50        34.65        11.57        15.09        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        49.22        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         2.37        14.50 
TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       42.15         1.64       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF 
       52.54        48.92        37.61        50.83         7.69        26.20 
TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 
       12.69        11.93        12.72        84.23        13.05        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U 
       37.81       112.11        35.90        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-A95F TCGA-YT-A95H 
       49.38       107.44        18.67        13.32        22.78        12.79 
TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 
        0.13         0.20        30.74        18.58        16.57        12.46 
TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E 
        0.66        10.68        60.33        43.43        42.81         0.23 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L 
        0.16        32.35        37.48         5.19        31.50         0.30 
TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V 
        0.46         1.81        10.68         7.17        35.34         8.52 
TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       28.04        38.30        16.34        68.91 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            10.36              0.13 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            97.41            149.98 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            49.78             30.41 
[1] "10.4 - 97.4 (49.8)" "0.1 - 150.0 (30.4)"
[1] "hr="     "7.5e+07"
D29V2, continuous
D29V3, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    1  6
  3Q LOSS WILD-TYPE 58 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    6
  3Q LOSS WILD-TYPE   58   56
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               1                58
  MALE                 6                56
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         0     6
  3Q LOSS WILD-TYPE    12                         6    94
D29V4, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   6                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"
D29V5, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    3  3
  3Q LOSS WILD-TYPE  6 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    3
  3Q LOSS WILD-TYPE    6   95
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 6
  NOT HISPANIC OR LATINO               3                95
[1] 2 2
[1] FALSE

Clustering(30) Variable = 4P LOSS MUTATION ANALYSIS
D30V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED     5   0
  4P LOSS WILD-TYPE 108   6
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                5               114 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                0                 6 
$`4P LOSS MUTATED`
TCGA-4V-A9QJ TCGA-4X-A9FD TCGA-XM-A8RC TCGA-XU-A930 TCGA-YT-A95G 
       88.83        39.45        97.41        82.65        49.78 

$`4P LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QL TCGA-4V-A9QM 
       13.48         9.96        34.52        89.23        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR 
       19.50        34.65        11.57        10.36        15.09        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        49.22        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         2.37        14.50 
TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       42.15         1.64       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF 
       52.54        48.92        37.61        50.83         7.69        26.20 
TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 
       12.69        11.93        12.72        84.23        13.05        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U 
       37.81       112.11        35.90        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-A95F 
       50.53        49.38       107.44        18.67        13.32        22.78 
TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 
       12.79         0.13         0.20        30.74        18.58        16.57 
TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D 
       12.46         0.66        10.68        60.33        43.43        42.81 
TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K 
        0.23         0.16        32.35        37.48         5.19        31.50 
TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
        0.30         0.46         1.81        10.68         7.17        35.34 
TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
        8.52        28.04        26.93        38.30        16.34        68.91 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            39.45              0.13 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            97.41            149.98 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            82.65             29.26 
[1] "39.5 - 97.4 (82.7)" "0.1 - 150.0 (29.3)"
[1] "hr="     "7.8e+07"
D30V2, continuous
D30V3, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    2  3
  4P LOSS WILD-TYPE 57 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      2    3
  4P LOSS WILD-TYPE   57   59
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               2                57
  MALE                 3                59
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       0                         0     5
  4P LOSS WILD-TYPE    13                         6    95
D30V4, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   5                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"
D30V5, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    0  4
  4P LOSS WILD-TYPE  9 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      0    4
  4P LOSS WILD-TYPE    9   94
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               4                94
[1] 2 2
[1] FALSE

Clustering(31) Variable = 4Q LOSS MUTATION ANALYSIS
D31V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED     4   0
  4Q LOSS WILD-TYPE 109   6
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4               115 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                0                 6 
$`4Q LOSS MUTATED`
TCGA-4V-A9QJ TCGA-XM-A8RC TCGA-XU-A930 TCGA-YT-A95G 
       88.83        97.41        82.65        49.78 

$`4Q LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QL TCGA-4V-A9QM 
       13.48         9.96        34.52        89.23        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F 
       39.45        19.50        34.65        11.57        10.36        15.09 
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        49.22 
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         2.37 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 
       14.50        42.15         1.64       125.19        54.08        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RD TCGA-XM-A8RE 
       30.08        52.54        48.92        37.61        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 
       26.20        12.69        11.93        12.72        84.23        13.05 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T 
       32.25        37.81       112.11        35.90        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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       22.78        12.79         0.13         0.20        30.74        18.58 
TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C 
       16.57        12.46         0.66        10.68        60.33        43.43 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I 
       42.81         0.23         0.16        32.35        37.48         5.19 
TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       31.50         0.30         0.46         1.81        10.68         7.17 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
       35.34         8.52        28.04        26.93        38.30        16.34 
TCGA-ZL-A9V6 
       68.91 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            49.78              0.13 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            97.41            149.98 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            85.74             29.62 
[1] "49.8 - 97.4 (85.7)" "0.1 - 150.0 (29.6)"
[1] "hr="     "7.8e+07"
D31V2, continuous
D31V3, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    1  3
  4Q LOSS WILD-TYPE 58 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    3
  4Q LOSS WILD-TYPE   58   59
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               1                58
  MALE                 3                59
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       0                         0     4
  4Q LOSS WILD-TYPE    13                         6    96
D31V4, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   4                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"
D31V5, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    0  3
  4Q LOSS WILD-TYPE  9 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      0    3
  4Q LOSS WILD-TYPE    9   95
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO               3                95
[1] 2 2
[1] FALSE

Clustering(32) Variable = 6P LOSS MUTATION ANALYSIS
D32V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   18  2
  6P LOSS WILD-TYPE 95  4
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               20                99 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2                 4 
$`6P LOSS MUTATED`
TCGA-3G-AB14 TCGA-3S-A8YW TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4X-A9FD TCGA-5G-A9ZZ 
       17.75        13.48        28.90        19.76        39.45        19.50 
TCGA-5U-AB0D TCGA-5U-AB0E TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XU-A92X TCGA-XU-A930 
       11.57        10.36        97.41        50.83        77.03        82.65 
TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A936 TCGA-YT-A95G TCGA-ZB-A961 TCGA-ZB-A96F 
       52.90        70.65        21.14        49.78         0.13         0.16 
TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       28.04        26.93 

$`6P LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-AAYX 
       56.65        59.15        81.80        90.61        15.35         9.96 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ 
       34.52        89.23        88.83        56.75        38.50        45.07 
TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 
       19.76        21.70        16.60        14.07        11.24        15.78 
TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-5K-AAAP TCGA-5U-AB0F TCGA-5V-A9RR 
       12.89        23.57        55.46        34.65        15.09        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        49.22        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         2.37        14.50 
TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       42.15         1.64       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG 
       52.54        48.92        37.61         7.69        26.20        12.69 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       11.93        12.72        84.23        13.05        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
      112.11        35.90        90.05        45.24       149.98         4.08 
TCGA-XU-A92W TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX 
      107.80       114.67       120.43        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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95H TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 
       22.78        12.79         0.20        30.74        18.58        16.57 
TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D 
       12.46         0.66        10.68        60.33        43.43        42.81 
TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L 
        0.23        32.35        37.48         5.19        31.50         0.30 
TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V 
        0.46         1.81        10.68         7.17        35.34         8.52 
TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       38.30        16.34        68.91 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.13              0.20 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            97.41            149.98 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           27.485            32.250 
[1] "0.1 - 97.4 (27.5)"  "0.2 - 150.0 (32.2)"
[1] "hr=" "3.8"
D32V2, continuous
D32V3, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    9 11
  6P LOSS WILD-TYPE 50 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      9   11
  6P LOSS WILD-TYPE   50   51
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               9                50
  MALE                11                51
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       2                         0    18
  6P LOSS WILD-TYPE    11                         6    82
D32V4, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   2                11
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  18                82
[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"
D32V5, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    5 13
  6P LOSS WILD-TYPE  4 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   13
  6P LOSS WILD-TYPE    4   85
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 4
  NOT HISPANIC OR LATINO              13                85
[1] 2 2
[1] FALSE

Clustering(33) Variable = 6Q LOSS MUTATION ANALYSIS
D33V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   17  2
  6Q LOSS WILD-TYPE 96  4
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               19               100 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                 4 
$`6Q LOSS MUTATED`
TCGA-3G-AB14 TCGA-3S-A8YW TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4X-A9FD TCGA-5G-A9ZZ 
       17.75        13.48        28.90        19.76        39.45        19.50 
TCGA-5U-AB0D TCGA-5U-AB0E TCGA-X7-A8M0 TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XU-A92X 
       11.57        10.36        14.50        97.41        50.83        77.03 
TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A936 TCGA-YT-A95G TCGA-ZB-A96F TCGA-ZC-AAA7 
       82.65        52.90        21.14        49.78         0.16        28.04 
TCGA-ZC-AAAA 
       26.93 

$`6Q LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-AAYX 
       56.65        59.15        81.80        90.61        15.35         9.96 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ 
       34.52        89.23        88.83        56.75        38.50        45.07 
TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 
       19.76        21.70        16.60        14.07        11.24        15.78 
TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-5K-AAAP TCGA-5U-AB0F TCGA-5V-A9RR 
       12.89        23.57        55.46        34.65        15.09        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        49.22        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         2.37        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
        1.64       125.19        54.08        83.28        30.08        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH 
       48.92        37.61         7.69        26.20        12.69        11.93 
TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O 
       12.72        84.23        13.05        32.25        37.81       112.11 
TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W 
       35.90        90.05        45.24       149.98         4.08       107.80 
TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX 
      114.67       120.43        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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       22.78        12.79         0.13         0.20        30.74        18.58 
TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C 
       16.57        12.46         0.66        10.68        60.33        43.43 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K 
       42.81         0.23        32.35        37.48         5.19        31.50 
TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
        0.30         0.46         1.81        10.68         7.17        35.34 
TCGA-ZB-A96V TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
        8.52        38.30        16.34        68.91 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.16              0.13 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            97.41            149.98 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            26.93             32.25 
[1] "0.2 - 97.4 (26.9)"  "0.1 - 150.0 (32.2)"
[1] "hr=" "4.1"
D33V2, continuous
D33V3, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   10  9
  6Q LOSS WILD-TYPE 49 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     10    9
  6Q LOSS WILD-TYPE   49   53
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              10                49
  MALE                 9                53
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       1                         0    18
  6Q LOSS WILD-TYPE    12                         6    82
D33V4, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   1                12
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  18                82
[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"
D33V5, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    5 12
  6Q LOSS WILD-TYPE  4 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      5   12
  6Q LOSS WILD-TYPE    4   86
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 4
  NOT HISPANIC OR LATINO              12                86
[1] 2 2
[1] FALSE

Clustering(34) Variable = 9P LOSS MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED     4   0
  9P LOSS WILD-TYPE 109   6
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                4               115 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                0                 6 
$`9P LOSS MUTATED`
TCGA-3S-A8YW TCGA-XU-A936 TCGA-ZB-A969 TCGA-ZB-A96L 
       13.48        21.14         0.66         0.30 

$`9P LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F 
       39.45        19.50        34.65        11.57        10.36        15.09 
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        49.22 
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         2.37 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 
       14.50        42.15         1.64       125.19        54.08        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD 
       30.08        52.54        48.92        37.61        97.41        50.83 
TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
        7.69        26.20        12.69        11.93        12.72        84.23 
TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R 
       13.05        32.25        37.81       112.11        35.90        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        18.67 
TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 
       13.32        22.78        49.78        12.79         0.13         0.20 
TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A96A TCGA-ZB-A96B 
       30.74        18.58        16.57        12.46        10.68        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H 
       43.43        42.81         0.23         0.16        32.35        37.48 
TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
        5.19        31.50         0.46         1.81        10.68         7.17 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
       35.34         8.52        28.04        26.93        38.30        16.34 
TCGA-ZL-A9V6 
       68.91 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.30              0.13 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            21.14            149.98 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             7.07             32.25 
[1] "0.3 - 21.1 (7.1)"   "0.1 - 150.0 (32.2)"
[1] "hr="     "3400000"
D34V2, continuous
D34V3, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    3  1
  9P LOSS WILD-TYPE 56 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      3    1
  9P LOSS WILD-TYPE   56   61
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               3                56
  MALE                 1                61
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       0                         0     4
  9P LOSS WILD-TYPE    13                         6    96
D34V4, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   4                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"
D34V5, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    1  3
  9P LOSS WILD-TYPE  8 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1    3
  9P LOSS WILD-TYPE    8   95
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO               3                95
[1] 2 2
[1] FALSE

Clustering(35) Variable = 10P LOSS MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED     3   0
  10P LOSS WILD-TYPE 110   6
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 3                116 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 0                  6 
$`10P LOSS MUTATED`
TCGA-5U-AB0D TCGA-X7-A8M0 TCGA-XM-A8RG 
       11.57        14.50        12.69 

$`10P LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT 
       38.50        28.90        45.07        19.76        19.76        21.70 
TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB 
       16.60        14.07        11.24        15.78        12.89        23.57 
TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0E TCGA-5U-AB0F 
       55.46        39.45        19.50        34.65        10.36        15.09 
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        49.22 
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         2.37 
TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       42.15         1.64       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE 
       52.54        48.92        37.61        97.41        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 
       26.20        11.93        12.72        84.23        13.05        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U 
       37.81       112.11        35.90        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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       22.78        49.78        12.79         0.13         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       18.58        16.57        12.46         0.66        10.68        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H 
       43.43        42.81         0.23         0.16        32.35        37.48 
TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
        5.19        31.50         0.30         0.46         1.81        10.68 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
        7.17        35.34         8.52        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 
       16.34        68.91 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             11.57               0.13 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             14.50             149.98 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            12.690             31.875 
[1] "11.6 - 14.5 (12.7)" "0.1 - 150.0 (31.9)"
[1] "hr="     "9200000"
D35V2, continuous
D35V3, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    2  1
  10P LOSS WILD-TYPE 57 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2    1
  10P LOSS WILD-TYPE   57   61
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                2                 57
  MALE                  1                 61
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       0                         0     3
  10P LOSS WILD-TYPE    13                         6    97
D35V4, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                 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"
D35V5, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    1  2
  10P LOSS WILD-TYPE  8 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1    2
  10P LOSS WILD-TYPE    8   96
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO                2                 96
[1] 2 2
[1] FALSE

Clustering(36) Variable = 11P LOSS MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED     9   0
  11P LOSS WILD-TYPE 104   6
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 9                110 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 0                  6 
$`11P LOSS MUTATED`
TCGA-4V-A9QN TCGA-4X-A9FD TCGA-5U-AB0D TCGA-5U-AB0E TCGA-XM-A8RC TCGA-XU-A92X 
       28.90        39.45        11.57        10.36        97.41        77.03 
TCGA-XU-A930 TCGA-ZB-A96I TCGA-ZC-AAAA 
       82.65         5.19        26.93 

$`11P LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       38.50        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 
       19.50        34.65        15.09        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        49.22        36.62        32.25        29.62 
TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 
       22.85        23.18         2.37        14.50        42.15         1.64 
TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      125.19        54.08        83.28        30.08        52.54        48.92 
TCGA-XM-A8RB TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH 
       37.61        50.83         7.69        26.20        12.69        11.93 
TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O 
       12.72        84.23        13.05        32.25        37.81       112.11 
TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W 
       35.90        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-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 
       18.67        13.32        22.78        49.78        12.79         0.13 
TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 
        0.20        30.74        18.58        16.57        12.46         0.66 
TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F 
       10.68        60.33        43.43        42.81         0.23         0.16 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O 
       32.35        37.48        31.50         0.30         0.46         1.81 
TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAF 
       10.68         7.17        35.34         8.52        28.04        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 
       16.34        68.91 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              5.19               0.13 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             97.41             149.98 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             28.90              31.12 
[1] "5.2 - 97.4 (28.9)"  "0.1 - 150.0 (31.1)"
[1] "hr="     "7.6e+07"
D36V2, continuous
D36V3, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    4  5
  11P LOSS WILD-TYPE 55 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4    5
  11P LOSS WILD-TYPE   55   57
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                4                 55
  MALE                  5                 57
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       1                         0     8
  11P LOSS WILD-TYPE    12                         6    92
D36V4, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    8                 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"
D36V5, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    4  5
  11P LOSS WILD-TYPE  5 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4    5
  11P LOSS WILD-TYPE    5   93
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO                5                 93
[1] 2 2
[1] FALSE

Clustering(37) Variable = 11Q LOSS MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED     7   0
  11Q LOSS WILD-TYPE 106   6
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                112 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 0                  6 
$`11Q LOSS MUTATED`
TCGA-4V-A9QN TCGA-4X-A9FD TCGA-5U-AB0E TCGA-XM-A8RC TCGA-XU-A92X TCGA-XU-A930 
       28.90        39.45        10.36        97.41        77.03        82.65 
TCGA-ZC-AAAA 
       26.93 

$`11Q LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       38.50        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 
       19.50        34.65        11.57        15.09        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        49.22        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         2.37        14.50        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
        1.64       125.19        54.08        83.28        30.08        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG 
       48.92        37.61        50.83         7.69        26.20        12.69 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       11.93        12.72        84.23        13.05        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
      112.11        35.90        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-A95F TCGA-YT-A95G TCGA-YT-A95H 
      107.44        18.67        13.32        22.78        49.78        12.79 
TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 
        0.13         0.20        30.74        18.58        16.57        12.46 
TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E 
        0.66        10.68        60.33        43.43        42.81         0.23 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L 
        0.16        32.35        37.48         5.19        31.50         0.30 
TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V 
        0.46         1.81        10.68         7.17        35.34         8.52 
TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       28.04        38.30        16.34        68.91 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             10.36               0.13 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             97.41             149.98 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             39.45              30.41 
[1] "10.4 - 97.4 (39.5)" "0.1 - 150.0 (30.4)"
[1] "hr="     "7.6e+07"
D37V2, continuous
D37V3, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    2  5
  11Q LOSS WILD-TYPE 57 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2    5
  11Q LOSS WILD-TYPE   57   57
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                2                 57
  MALE                  5                 57
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       1                         0     6
  11Q LOSS WILD-TYPE    12                         6    94
D37V4, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    6                 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"
D37V5, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    3  4
  11Q LOSS WILD-TYPE  6 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3    4
  11Q LOSS WILD-TYPE    6   94
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO                4                 94
[1] 2 2
[1] FALSE

Clustering(38) Variable = 12P LOSS MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED     8   0
  12P LOSS WILD-TYPE 105   6
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 8                111 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 0                  6 
$`12P LOSS MUTATED`
TCGA-4V-A9QQ TCGA-4X-A9FD TCGA-5U-AB0E TCGA-XU-A92X TCGA-XU-A930 TCGA-ZB-A961 
       45.07        39.45        10.36        77.03        82.65         0.13 
TCGA-ZB-A96F TCGA-ZC-AAAA 
        0.16        26.93 

$`12P LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       38.50        28.90        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 
       19.50        34.65        11.57        15.09        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        49.22        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         2.37        14.50        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
        1.64       125.19        54.08        83.28        30.08        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF 
       48.92        37.61        97.41        50.83         7.69        26.20 
TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 
       12.69        11.93        12.72        84.23        13.05        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U 
       37.81       112.11        35.90        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-A95F TCGA-YT-A95G 
       49.38       107.44        18.67        13.32        22.78        49.78 
TCGA-YT-A95H TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 
       12.79         0.20        30.74        18.58        16.57        12.46 
TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E 
        0.66        10.68        60.33        43.43        42.81         0.23 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M 
       32.35        37.48         5.19        31.50         0.30         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
        1.81        10.68         7.17        35.34         8.52        28.04 
TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       38.30        16.34        68.91 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.13               0.20 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             82.65             149.98 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             33.19              30.74 
[1] "0.1 - 82.7 (33.2)"  "0.2 - 150.0 (30.7)"
[1] "hr="     "2.7e+07"
D38V2, continuous
D38V3, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    2  6
  12P LOSS WILD-TYPE 57 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2    6
  12P LOSS WILD-TYPE   57   56
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                2                 57
  MALE                  6                 56
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       1                         0     7
  12P LOSS WILD-TYPE    12                         6    93
D38V4, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    7                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V5, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    2  6
  12P LOSS WILD-TYPE  7 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2    6
  12P LOSS WILD-TYPE    7   92
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO                6                 92
[1] 2 2
[1] FALSE

Clustering(39) Variable = 12Q LOSS MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED     7   0
  12Q LOSS WILD-TYPE 106   6
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 7                112 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 0                  6 
$`12Q LOSS MUTATED`
TCGA-4X-A9FD TCGA-5U-AB0E TCGA-XU-A92X TCGA-XU-A930 TCGA-ZB-A961 TCGA-ZB-A96F 
       39.45        10.36        77.03        82.65         0.13         0.16 
TCGA-ZC-AAAA 
       26.93 

$`12Q LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT 
       38.50        28.90        45.07        19.76        19.76        21.70 
TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB 
       16.60        14.07        11.24        15.78        12.89        23.57 
TCGA-4X-A9FC TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0F TCGA-5V-A9RR 
       55.46        19.50        34.65        11.57        15.09        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        49.22        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         2.37        14.50 
TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       42.15         1.64       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE 
       52.54        48.92        37.61        97.41        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 
       26.20        12.69        11.93        12.72        84.23        13.05 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T 
       32.25        37.81       112.11        35.90        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-A95F 
       50.53        49.38       107.44        18.67        13.32        22.78 
TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 
       49.78        12.79         0.20        30.74        18.58        16.57 
TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D 
       12.46         0.66        10.68        60.33        43.43        42.81 
TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L 
        0.23        32.35        37.48         5.19        31.50         0.30 
TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V 
        0.46         1.81        10.68         7.17        35.34         8.52 
TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       28.04        38.30        16.34        68.91 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.13               0.20 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             82.65             149.98 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             26.93              31.12 
[1] "0.1 - 82.7 (26.9)"  "0.2 - 150.0 (31.1)"
[1] "hr="     "2.6e+07"
D39V2, continuous
D39V3, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    1  6
  12Q LOSS WILD-TYPE 58 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1    6
  12Q LOSS WILD-TYPE   58   56
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                1                 58
  MALE                  6                 56
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       1                         0     6
  12Q LOSS WILD-TYPE    12                         6    94
D39V4, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    6                 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"
D39V5, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    2  5
  12Q LOSS WILD-TYPE  7 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    5
  12Q LOSS WILD-TYPE    7   93
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO                5                 93
[1] 2 2
[1] FALSE

Clustering(40) Variable = 13Q LOSS MUTATION ANALYSIS
D40V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    13   0
  13Q LOSS WILD-TYPE 100   6
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                13                106 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 0                  6 
$`13Q LOSS MUTATED`
TCGA-3S-A8YW TCGA-4V-A9QJ TCGA-4V-A9QX TCGA-4X-A9FD TCGA-5U-AB0E TCGA-XM-A8RC 
       13.48        88.83        11.24        39.45        10.36        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        18.67        49.78         5.19 
TCGA-ZC-AAAA 
       26.93 

$`13Q LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN 
        9.96        34.52        89.23        56.75        38.50        28.90 
TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW 
       45.07        19.76        19.76        21.70        16.60        14.07 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-5G-A9ZZ TCGA-5K-AAAP 
       15.78        12.89        23.57        55.46        19.50        34.65 
TCGA-5U-AB0D TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 
       11.57        15.09        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        49.22        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         2.37        14.50        42.15         1.64       125.19 
TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       54.08        83.28        30.08        52.54        48.92        37.61 
TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI 
       50.83         7.69        26.20        12.69        11.93        12.72 
TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q 
       84.23        13.05        32.25        37.81       112.11        35.90 
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-A95F 
       62.17        50.53        49.38       107.44        13.32        22.78 
TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 
       12.79         0.13         0.20        30.74        18.58        16.57 
TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D 
       12.46         0.66        10.68        60.33        43.43        42.81 
TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96K TCGA-ZB-A96L 
        0.23         0.16        32.35        37.48        31.50         0.30 
TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V 
        0.46         1.81        10.68         7.17        35.34         8.52 
TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       28.04        38.30        16.34        68.91 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              5.19               0.13 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             97.41             149.98 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             39.45              30.41 
[1] "5.2 - 97.4 (39.5)"  "0.1 - 150.0 (30.4)"
[1] "hr="     "8.3e+07"
D40V2, continuous
D40V3, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    6  8
  13Q LOSS WILD-TYPE 53 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      6    8
  13Q LOSS WILD-TYPE   53   54
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                6                 53
  MALE                  8                 54
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       2                         0    12
  13Q LOSS WILD-TYPE    11                         6    88
D40V4, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    2                 11
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                   12                 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"
D40V5, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    3  9
  13Q LOSS WILD-TYPE  6 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3    9
  13Q LOSS WILD-TYPE    6   89
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO                9                 89
[1] 2 2
[1] FALSE

Clustering(41) Variable = 16P LOSS MUTATION ANALYSIS
D41V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     5   0
  16P LOSS WILD-TYPE 108   6
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                114 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 0                  6 
$`16P LOSS MUTATED`
TCGA-3S-A8YW TCGA-XH-A853 TCGA-XU-A930 TCGA-XU-A936 TCGA-ZC-AAAA 
       13.48        30.08        82.65        21.14        26.93 

$`16P LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F 
       39.45        19.50        34.65        11.57        10.36        15.09 
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        49.22 
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         2.37 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 
       14.50        42.15         1.64       125.19        54.08        83.28 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE 
       52.54        48.92        37.61        97.41        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 
       26.20        12.69        11.93        12.72        84.23        13.05 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T 
       32.25        37.81       112.11        35.90        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-A95F 
       50.53        49.38       107.44        18.67        13.32        22.78 
TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       49.78        12.79         0.13         0.20        30.74        18.58 
TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C 
       16.57        12.46         0.66        10.68        60.33        43.43 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I 
       42.81         0.23         0.16        32.35        37.48         5.19 
TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       31.50         0.30         0.46         1.81        10.68         7.17 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       35.34         8.52        28.04        38.30        16.34        68.91 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             13.48               0.13 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             82.65             149.98 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            26.930             31.875 
[1] "13.5 - 82.7 (26.9)" "0.1 - 150.0 (31.9)"
[1] "hr="     "2.6e+07"
D41V2, continuous
D41V3, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  4
  16P LOSS WILD-TYPE 58 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    4
  16P LOSS WILD-TYPE   58   58
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                1                 58
  MALE                  4                 58
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       0                         1     4
  16P LOSS WILD-TYPE    13                         5    96
D41V4, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                    4                 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"
D41V5, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    2  3
  16P LOSS WILD-TYPE  7 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2    3
  16P LOSS WILD-TYPE    7   95
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO                3                 95
[1] 2 2
[1] FALSE

Clustering(42) Variable = 16Q LOSS MUTATION ANALYSIS
D42V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    11   2
  16Q LOSS WILD-TYPE 102   4
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                13                106 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                  4 
$`16Q LOSS MUTATED`
TCGA-3S-A8YW TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-XH-A853 TCGA-XU-A930 
       13.48        39.45        19.50        11.57        30.08        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         0.66         8.52        28.04 
TCGA-ZC-AAAA 
       26.93 

$`16Q LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-5K-AAAP TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 
       34.65        10.36        15.09        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        49.22        36.62        32.25        29.62 
TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 
       22.85        23.18         2.37        14.50        42.15         1.64 
TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
      125.19        54.08        83.28        52.54        48.92        37.61 
TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH 
       97.41        50.83         7.69        26.20        12.69        11.93 
TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O 
       12.72        84.23        13.05        32.25        37.81       112.11 
TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W 
       35.90        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        18.67 
TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 
       13.32        22.78        49.78        12.79         0.13         0.20 
TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C 
       30.74        18.58        16.57        10.68        60.33        43.43 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I 
       42.81         0.23         0.16        32.35        37.48         5.19 
TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       31.50         0.30         0.46         1.81        10.68         7.17 
TCGA-ZB-A96R TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       35.34        38.30        16.34        68.91 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.66               0.13 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             82.65             149.98 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             21.14              32.30 
[1] "0.7 - 82.7 (21.1)"  "0.1 - 150.0 (32.3)"
[1] "hr=" "7.7"
D42V2, continuous
D42V3, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    7  6
  16Q LOSS WILD-TYPE 52 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      7    6
  16Q LOSS WILD-TYPE   52   56
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                7                 52
  MALE                  6                 56
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       1                         1    11
  16Q LOSS WILD-TYPE    12                         5    89
D42V4, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   11                 89
[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"
D42V5, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    3 10
  16Q LOSS WILD-TYPE  6 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3   10
  16Q LOSS WILD-TYPE    6   88
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO               10                 88
[1] 2 2
[1] FALSE

Clustering(43) Variable = 17P LOSS MUTATION ANALYSIS
D43V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   14  0
  17P LOSS WILD-TYPE 99  6
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                14                105 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 0                  6 
$`17P LOSS MUTATED`
TCGA-3S-A8YW TCGA-4V-A9QJ TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-5U-AB0E 
       13.48        88.83        39.45        19.50        11.57        10.36 
TCGA-XM-A8RG TCGA-XU-A92X TCGA-XU-A933 TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A96F 
       12.69        77.03        58.82         0.13         0.20         0.16 
TCGA-ZB-A96L TCGA-ZC-AAAA 
        0.30        26.93 

$`17P LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN 
        9.96        34.52        89.23        56.75        38.50        28.90 
TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW 
       45.07        19.76        19.76        21.70        16.60        14.07 
TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-5K-AAAP 
       11.24        15.78        12.89        23.57        55.46        34.65 
TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB 
       15.09        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 
       49.22        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 
        2.37        14.50        42.15         1.64       125.19        54.08 
TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC 
       83.28        30.08        52.54        48.92        37.61        97.41 
TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
       50.83         7.69        26.20        11.93        12.72        84.23 
TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R 
       13.05        32.25        37.81       112.11        35.90        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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 
       22.78        49.78        12.79        30.74        18.58        16.57 
TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D 
       12.46         0.66        10.68        60.33        43.43        42.81 
TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96M 
        0.23        32.35        37.48         5.19        31.50         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
        1.81        10.68         7.17        35.34         8.52        28.04 
TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       38.30        16.34        68.91 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.13               0.23 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             88.83             149.98 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            13.085             32.250 
[1] "0.1 - 88.8 (13.1)"  "0.2 - 150.0 (32.2)"
[1] "hr="     "7.5e+07"
D43V2, continuous
D43V3, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    5  9
  17P LOSS WILD-TYPE 54 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      5    9
  17P LOSS WILD-TYPE   54   53
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                5                 54
  MALE                  9                 53
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       2                         0    12
  17P LOSS WILD-TYPE    11                         6    88
D43V4, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    2                 11
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                   12                 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"
D43V5, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    4 10
  17P LOSS WILD-TYPE  5 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4   10
  17P LOSS WILD-TYPE    5   88
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO               10                 88
[1] 2 2
[1] FALSE

Clustering(44) Variable = 17Q LOSS MUTATION ANALYSIS
D44V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED     6   0
  17Q LOSS WILD-TYPE 107   6
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 6                113 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 0                  6 
$`17Q LOSS MUTATED`
TCGA-3S-A8YW TCGA-4X-A9FD TCGA-5U-AB0E TCGA-XU-A92X TCGA-ZB-A96L TCGA-ZC-AAAA 
       13.48        39.45        10.36        77.03         0.30        26.93 

$`17Q LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 
       19.50        34.65        11.57        15.09        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        49.22        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         2.37        14.50        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
        1.64       125.19        54.08        83.28        30.08        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF 
       48.92        37.61        97.41        50.83         7.69        26.20 
TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 
       12.69        11.93        12.72        84.23        13.05        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U 
       37.81       112.11        35.90        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-A95F 
       50.53        49.38       107.44        18.67        13.32        22.78 
TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       49.78        12.79         0.13         0.20        30.74        18.58 
TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C 
       16.57        12.46         0.66        10.68        60.33        43.43 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I 
       42.81         0.23         0.16        32.35        37.48         5.19 
TCGA-ZB-A96K TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
       31.50         0.46         1.81        10.68         7.17        35.34 
TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
        8.52        28.04        38.30        16.34        68.91 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.30               0.13 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             77.03             149.98 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            20.205             31.500 
[1] "0.3 - 77.0 (20.2)"  "0.1 - 150.0 (31.5)"
[1] "hr="     "2.6e+07"
D44V2, continuous
D44V3, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    2  4
  17Q LOSS WILD-TYPE 57 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    4
  17Q LOSS WILD-TYPE   57   58
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                2                 57
  MALE                  4                 58
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       1                         0     5
  17Q LOSS WILD-TYPE    12                         6    95
D44V4, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    5                 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"
D44V5, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    3  3
  17Q LOSS WILD-TYPE  6 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3    3
  17Q LOSS WILD-TYPE    6   95
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO                3                 95
[1] 2 2
[1] FALSE

Clustering(45) Variable = 18P LOSS MUTATION ANALYSIS
D45V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED     6   1
  18P LOSS WILD-TYPE 107   5
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                112 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                  5 
$`18P LOSS MUTATED`
TCGA-4X-A9FD TCGA-5U-AB0D TCGA-5U-AB0E TCGA-XM-A8RD TCGA-XU-A930 TCGA-XU-A931 
       39.45        11.57        10.36        50.83        82.65        52.90 
TCGA-ZB-A961 
        0.13 

$`18P LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT 
       38.50        28.90        45.07        19.76        19.76        21.70 
TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB 
       16.60        14.07        11.24        15.78        12.89        23.57 
TCGA-4X-A9FC TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 
       55.46        19.50        34.65        15.09        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        49.22        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         2.37        14.50        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
        1.64       125.19        54.08        83.28        30.08        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG 
       48.92        37.61        97.41         7.69        26.20        12.69 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       11.93        12.72        84.23        13.05        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
      112.11        35.90        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-A95F TCGA-YT-A95G TCGA-YT-A95H 
      107.44        18.67        13.32        22.78        49.78        12.79 
TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 
        0.20        30.74        18.58        16.57        12.46         0.66 
TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F 
       10.68        60.33        43.43        42.81         0.23         0.16 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M 
       32.35        37.48         5.19        31.50         0.30         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
        1.81        10.68         7.17        35.34         8.52        28.04 
TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       26.93        38.30        16.34        68.91 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.13               0.16 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             82.65             149.98 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             39.45              30.41 
[1] "0.1 - 82.7 (39.5)"  "0.2 - 150.0 (30.4)"
[1] "hr=" "4.3"
D45V2, continuous
D45V3, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    4  3
  18P LOSS WILD-TYPE 55 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4    3
  18P LOSS WILD-TYPE   55   59
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                4                 55
  MALE                  3                 59
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       0                         0     7
  18P LOSS WILD-TYPE    13                         6    93
D45V4, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    7                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V5, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2  4
  18P LOSS WILD-TYPE  7 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    4
  18P LOSS WILD-TYPE    7   94
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO                4                 94
[1] 2 2
[1] FALSE

Clustering(46) Variable = 18Q LOSS MUTATION ANALYSIS
D46V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED     6   1
  18Q LOSS WILD-TYPE 107   5
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                112 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 1                  5 
$`18Q LOSS MUTATED`
TCGA-4X-A9FD TCGA-5U-AB0D TCGA-5U-AB0E TCGA-XM-A8RD TCGA-XU-A930 TCGA-XU-A931 
       39.45        11.57        10.36        50.83        82.65        52.90 
TCGA-ZB-A961 
        0.13 

$`18Q LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT 
       38.50        28.90        45.07        19.76        19.76        21.70 
TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB 
       16.60        14.07        11.24        15.78        12.89        23.57 
TCGA-4X-A9FC TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 
       55.46        19.50        34.65        15.09        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        49.22        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         2.37        14.50        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
        1.64       125.19        54.08        83.28        30.08        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG 
       48.92        37.61        97.41         7.69        26.20        12.69 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       11.93        12.72        84.23        13.05        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
      112.11        35.90        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-A95F TCGA-YT-A95G TCGA-YT-A95H 
      107.44        18.67        13.32        22.78        49.78        12.79 
TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 
        0.20        30.74        18.58        16.57        12.46         0.66 
TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F 
       10.68        60.33        43.43        42.81         0.23         0.16 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M 
       32.35        37.48         5.19        31.50         0.30         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
        1.81        10.68         7.17        35.34         8.52        28.04 
TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       26.93        38.30        16.34        68.91 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.13               0.16 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             82.65             149.98 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             39.45              30.41 
[1] "0.1 - 82.7 (39.5)"  "0.2 - 150.0 (30.4)"
[1] "hr=" "4.3"
D46V2, continuous
D46V3, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    4  3
  18Q LOSS WILD-TYPE 55 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4    3
  18Q LOSS WILD-TYPE   55   59
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                4                 55
  MALE                  3                 59
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       0                         0     7
  18Q LOSS WILD-TYPE    13                         6    93
D46V4, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    7                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V5, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    2  4
  18Q LOSS WILD-TYPE  7 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2    4
  18Q LOSS WILD-TYPE    7   94
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO                4                 94
[1] 2 2
[1] FALSE

Clustering(47) Variable = 19P LOSS MUTATION ANALYSIS
D47V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED     3   0
  19P LOSS WILD-TYPE 110   6
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                116 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 0                  6 
$`19P LOSS MUTATED`
TCGA-3S-A8YW TCGA-5U-AB0D TCGA-XU-A936 
       13.48        11.57        21.14 

$`19P LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR 
       39.45        19.50        34.65        10.36        15.09        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        49.22        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         2.37        14.50 
TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       42.15         1.64       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE 
       52.54        48.92        37.61        97.41        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 
       26.20        12.69        11.93        12.72        84.23        13.05 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T 
       32.25        37.81       112.11        35.90        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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       22.78        49.78        12.79         0.13         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       18.58        16.57        12.46         0.66        10.68        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H 
       43.43        42.81         0.23         0.16        32.35        37.48 
TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
        5.19        31.50         0.30         0.46         1.81        10.68 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
        7.17        35.34         8.52        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 
       16.34        68.91 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             11.57               0.13 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             21.14             149.98 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            13.480             31.875 
[1] "11.6 - 21.1 (13.5)" "0.1 - 150.0 (31.9)"
[1] "hr="     "9200000"
D47V2, continuous
D47V3, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    2  1
  19P LOSS WILD-TYPE 57 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    1
  19P LOSS WILD-TYPE   57   61
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                2                 57
  MALE                  1                 61
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       0                         0     3
  19P LOSS WILD-TYPE    13                         6    97
D47V4, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                 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"
D47V5, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    2  1
  19P LOSS WILD-TYPE  7 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    1
  19P LOSS WILD-TYPE    7   97
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO                1                 97
[1] 2 2
[1] FALSE

Clustering(48) Variable = 19Q LOSS MUTATION ANALYSIS
D48V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED     3   0
  19Q LOSS WILD-TYPE 110   6
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                116 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 0                  6 
$`19Q LOSS MUTATED`
TCGA-3S-A8YW TCGA-5U-AB0D TCGA-XU-A936 
       13.48        11.57        21.14 

$`19Q LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR 
       39.45        19.50        34.65        10.36        15.09        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        49.22        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         2.37        14.50 
TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       42.15         1.64       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE 
       52.54        48.92        37.61        97.41        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 
       26.20        12.69        11.93        12.72        84.23        13.05 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T 
       32.25        37.81       112.11        35.90        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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       22.78        49.78        12.79         0.13         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       18.58        16.57        12.46         0.66        10.68        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H 
       43.43        42.81         0.23         0.16        32.35        37.48 
TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
        5.19        31.50         0.30         0.46         1.81        10.68 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
        7.17        35.34         8.52        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 
       16.34        68.91 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             11.57               0.13 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             21.14             149.98 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            13.480             31.875 
[1] "11.6 - 21.1 (13.5)" "0.1 - 150.0 (31.9)"
[1] "hr="     "9200000"
D48V2, continuous
D48V3, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2  1
  19Q LOSS WILD-TYPE 57 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    1
  19Q LOSS WILD-TYPE   57   61
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                2                 57
  MALE                  1                 61
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       0                         0     3
  19Q LOSS WILD-TYPE    13                         6    97
D48V4, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    0                 13
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                 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"
D48V5, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2  1
  19Q LOSS WILD-TYPE  7 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    1
  19Q LOSS WILD-TYPE    7   97
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO                1                 97
[1] 2 2
[1] FALSE

Clustering(49) Variable = 21Q LOSS MUTATION ANALYSIS
D49V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED     9   0
  21Q LOSS WILD-TYPE 104   6
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 9                110 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 0                  6 
$`21Q LOSS MUTATED`
TCGA-4V-A9QR TCGA-4X-A9FD TCGA-5U-AB0D TCGA-5U-AB0E TCGA-XU-A92X TCGA-XU-A930 
       19.76        39.45        11.57        10.36        77.03        82.65 
TCGA-ZB-A96F TCGA-ZB-A96I TCGA-ZC-AAAA 
        0.16         5.19        26.93 

$`21Q LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       38.50        28.90        45.07        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 
       19.50        34.65        15.09        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        49.22        36.62        32.25        29.62 
TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 
       22.85        23.18         2.37        14.50        42.15         1.64 
TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      125.19        54.08        83.28        30.08        52.54        48.92 
TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG 
       37.61        97.41        50.83         7.69        26.20        12.69 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       11.93        12.72        84.23        13.05        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
      112.11        35.90        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-A95F TCGA-YT-A95G TCGA-YT-A95H 
      107.44        18.67        13.32        22.78        49.78        12.79 
TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 
        0.13         0.20        30.74        18.58        16.57        12.46 
TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E 
        0.66        10.68        60.33        43.43        42.81         0.23 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O 
       32.35        37.48        31.50         0.30         0.46         1.81 
TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAF 
       10.68         7.17        35.34         8.52        28.04        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 
       16.34        68.91 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.16               0.13 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             82.65             149.98 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            19.760             31.875 
[1] "0.2 - 82.7 (19.8)"  "0.1 - 150.0 (31.9)"
[1] "hr="     "2.7e+07"
D49V2, continuous
D49V3, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    4  5
  21Q LOSS WILD-TYPE 55 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4    5
  21Q LOSS WILD-TYPE   55   57
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                4                 55
  MALE                  5                 57
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       1                         0     8
  21Q LOSS WILD-TYPE    12                         6    92
D49V4, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    8                 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"
D49V5, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    3  6
  21Q LOSS WILD-TYPE  6 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3    6
  21Q LOSS WILD-TYPE    6   92
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO                6                 92
[1] 2 2
[1] FALSE

Clustering(50) Variable = 22Q LOSS MUTATION ANALYSIS
D50V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    12   0
  22Q LOSS WILD-TYPE 101   6
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                12                107 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 0                  6 
$`22Q LOSS MUTATED`
TCGA-3G-AB19 TCGA-3S-A8YW TCGA-4V-A9QJ TCGA-4V-A9QN TCGA-4V-A9QX TCGA-5U-AB0D 
       90.61        13.48        88.83        28.90        11.24        11.57 
TCGA-5U-AB0F TCGA-XM-A8RC TCGA-XU-A92Z TCGA-XU-A936 TCGA-ZB-A963 TCGA-ZB-A96A 
       15.09        97.41       120.43        21.14        30.74        10.68 

$`22Q LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-AAYX 
       56.65        59.15        81.80        17.75        15.35         9.96 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QR 
       34.52        89.23        56.75        38.50        45.07        19.76 
TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4X-A9F9 TCGA-4X-A9FA 
       19.76        21.70        16.60        14.07        15.78        12.89 
TCGA-4X-A9FB TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0E 
       23.57        55.46        39.45        19.50        34.65        10.36 
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        49.22 
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         2.37 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 
       14.50        42.15         1.64       125.19        54.08        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RD TCGA-XM-A8RE 
       30.08        52.54        48.92        37.61        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 
       26.20        12.69        11.93        12.72        84.23        13.05 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T 
       32.25        37.81       112.11        35.90        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-A95F 
       50.53        49.38       107.44        18.67        13.32        22.78 
TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A964 TCGA-ZB-A965 
       49.78        12.79         0.13         0.20        18.58        16.57 
TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46         0.66        60.33        43.43        42.81         0.23 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L 
        0.16        32.35        37.48         5.19        31.50         0.30 
TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V 
        0.46         1.81        10.68         7.17        35.34         8.52 
TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       28.04        26.93        38.30        16.34        68.91 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             10.68               0.13 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            120.43             149.98 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             25.02              32.25 
[1] "10.7 - 120.4 (25.0)" "0.1 - 150.0 (32.2)" 
[1] "hr="     "8.5e+07"
D50V2, continuous
D50V3, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    7  6
  22Q LOSS WILD-TYPE 52 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      7    6
  22Q LOSS WILD-TYPE   52   56
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                7                 52
  MALE                  6                 56
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       1                         0    12
  22Q LOSS WILD-TYPE    12                         6    88
D50V4, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    1                 12
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                   12                 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"
D50V5, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    4  9
  22Q LOSS WILD-TYPE  5 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4    9
  22Q LOSS WILD-TYPE    5   89
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO                9                 89
[1] 2 2
[1] FALSE

Clustering(51) Variable = XP LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED     5   2
  XP LOSS WILD-TYPE 108   4
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                7               112 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                2                 4 
$`XP LOSS MUTATED`
TCGA-3G-AB0T TCGA-3S-A8YW TCGA-4V-A9QJ TCGA-4V-A9QN TCGA-4X-A9FD TCGA-XU-A931 
       81.80        13.48        88.83        28.90        39.45        52.90 
TCGA-ZB-A96F 
        0.16 

$`XP LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-AAYX 
       56.65        59.15        17.75        90.61        15.35         9.96 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QR 
       34.52        89.23        56.75        38.50        45.07        19.76 
TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 
       19.76        21.70        16.60        14.07        11.24        15.78 
TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D 
       12.89        23.57        55.46        19.50        34.65        11.57 
TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 
       10.36        15.09        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        49.22        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         2.37        14.50        42.15         1.64       125.19 
TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       54.08        83.28        30.08        52.54        48.92        37.61 
TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH 
       97.41        50.83         7.69        26.20        12.69        11.93 
TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O 
       12.72        84.23        13.05        32.25        37.81       112.11 
TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W 
       35.90        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-A95F TCGA-YT-A95G TCGA-YT-A95H 
      107.44        18.67        13.32        22.78        49.78        12.79 
TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 
        0.13         0.20        30.74        18.58        16.57        12.46 
TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E 
        0.66        10.68        60.33        43.43        42.81         0.23 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M 
       32.35        37.48         5.19        31.50         0.30         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
        1.81        10.68         7.17        35.34         8.52        28.04 
TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       26.93        38.30        16.34        68.91 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.16              0.13 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            88.83            149.98 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            39.45             30.41 
[1] "0.2 - 88.8 (39.5)"  "0.1 - 150.0 (30.4)"
[1] "hr=" "7.9"
D51V2, continuous
D51V3, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    3  4
  XP LOSS WILD-TYPE 56 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      3    4
  XP LOSS WILD-TYPE   56   58
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE               3                56
  MALE                 4                58
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       0                         0     7
  XP LOSS WILD-TYPE    13                         6    93
D51V4, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   7                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V5, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    2  4
  XP LOSS WILD-TYPE  7 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2    4
  XP LOSS WILD-TYPE    7   94
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO               4                94
[1] 2 2
[1] FALSE

Clustering(52) Variable = XQ LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED     3   1
  XQ LOSS WILD-TYPE 110   5
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4               115 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                 5 
$`XQ LOSS MUTATED`
TCGA-3S-A8YW TCGA-4V-A9QN TCGA-4X-A9FD TCGA-XU-A931 
       13.48        28.90        39.45        52.90 

$`XQ LOSS WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW 
       45.07        19.76        19.76        21.70        16.60        14.07 
TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-5G-A9ZZ 
       11.24        15.78        12.89        23.57        55.46        19.50 
TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 
       34.65        11.57        10.36        15.09        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        49.22        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         2.37        14.50        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
        1.64       125.19        54.08        83.28        30.08        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF 
       48.92        37.61        97.41        50.83         7.69        26.20 
TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 
       12.69        11.93        12.72        84.23        13.05        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U 
       37.81       112.11        35.90        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-A95F 
       50.53        49.38       107.44        18.67        13.32        22.78 
TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       49.78        12.79         0.13         0.20        30.74        18.58 
TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C 
       16.57        12.46         0.66        10.68        60.33        43.43 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I 
       42.81         0.23         0.16        32.35        37.48         5.19 
TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       31.50         0.30         0.46         1.81        10.68         7.17 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
       35.34         8.52        28.04        26.93        38.30        16.34 
TCGA-ZL-A9V6 
       68.91 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            13.48              0.13 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            52.90            149.98 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           34.175            30.740 
[1] "13.5 - 52.9 (34.2)" "0.1 - 150.0 (30.7)"
[1] "hr=" "8.2"
D52V2, continuous
D52V3, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    3  1
  XQ LOSS WILD-TYPE 56 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3    1
  XQ LOSS WILD-TYPE   56   61
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               3                56
  MALE                 1                61
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       0                         0     4
  XQ LOSS WILD-TYPE    13                         6    96
D52V4, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   0                13
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   4                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"
D52V5, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    2  1
  XQ LOSS WILD-TYPE  7 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2    1
  XQ LOSS WILD-TYPE    7   97
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO               1                97
[1] 2 2
[1] FALSE
