[1] "ofn"       "-oTGBM-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/GBM-TP/22506586/GBM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBM-TP/22811914/transformed.cor.cli.txt"

nPatients in clinical file=595, in cluster file=283, common to both=280
[1]  36 280
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            80            200 
  TP53 MUTATED TP53 WILD-TYPE 
            80            200 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              32              248 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              32              248 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           24           256 
  RB1 MUTATED RB1 WILD-TYPE 
           24           256 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           29           251 
  NF1 MUTATED NF1 WILD-TYPE 
           29           251 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            86            194 
  PTEN MUTATED PTEN WILD-TYPE 
            86            194 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
            14            266 
  IDH1 MUTATED IDH1 WILD-TYPE 
            14            266 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26              254 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26              254 
[1] "STAG2 MUTATION ANALYSIS"
[1] 3
  STAG2 MUTATED STAG2 WILD-TYPE 
             12             268 
  STAG2 MUTATED STAG2 WILD-TYPE 
             12             268 
[1] "SLC26A3 MUTATION ANALYSIS"
[1] 3
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
                7               273 
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
                7               273 
[1] "SEMG1 MUTATION ANALYSIS"
[1] 3
  SEMG1 MUTATED SEMG1 WILD-TYPE 
              8             272 
  SEMG1 MUTATED SEMG1 WILD-TYPE 
              8             272 
[1] "KDR MUTATION ANALYSIS"
[1] 3
  KDR MUTATED KDR WILD-TYPE 
            8           272 
  KDR MUTATED KDR WILD-TYPE 
            8           272 
[1] "RPL5 MUTATION ANALYSIS"
[1] 3
  RPL5 MUTATED RPL5 WILD-TYPE 
             7            273 
  RPL5 MUTATED RPL5 WILD-TYPE 
             7            273 
[1] "ATRX MUTATION ANALYSIS"
[1] 3
  ATRX MUTATED ATRX WILD-TYPE 
            16            264 
  ATRX MUTATED ATRX WILD-TYPE 
            16            264 
[1] "MAP3K1 MUTATION ANALYSIS"
[1] 3
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
               6              274 
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
               6              274 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
             6            274 
  BRAF MUTATED BRAF WILD-TYPE 
             6            274 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
            73            207 
  EGFR MUTATED EGFR WILD-TYPE 
            73            207 
[1] "TMPRSS6 MUTATION ANALYSIS"
[1] 3
  TMPRSS6 MUTATED TMPRSS6 WILD-TYPE 
                6               274 
  TMPRSS6 MUTATED TMPRSS6 WILD-TYPE 
                6               274 
[1] "PRKCD MUTATION ANALYSIS"
[1] 3
  PRKCD MUTATED PRKCD WILD-TYPE 
              3             277 
  PRKCD MUTATED PRKCD WILD-TYPE 
              3             277 
[1] "TP63 MUTATION ANALYSIS"
[1] 3
  TP63 MUTATED TP63 WILD-TYPE 
             6            274 
  TP63 MUTATED TP63 WILD-TYPE 
             6            274 
[1] "PDGFRA MUTATION ANALYSIS"
[1] 3
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              11              269 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              11              269 
[1] "CHD8 MUTATION ANALYSIS"
[1] 3
  CHD8 MUTATED CHD8 WILD-TYPE 
             8            272 
  CHD8 MUTATED CHD8 WILD-TYPE 
             8            272 
[1] "IL4R MUTATION ANALYSIS"
[1] 3
  IL4R MUTATED IL4R WILD-TYPE 
             8            272 
  IL4R MUTATED IL4R WILD-TYPE 
             8            272 
[1] "REN MUTATION ANALYSIS"
[1] 3
  REN MUTATED REN WILD-TYPE 
            5           275 
  REN MUTATED REN WILD-TYPE 
            5           275 
[1] "CD209 MUTATION ANALYSIS"
[1] 3
  CD209 MUTATED CD209 WILD-TYPE 
              5             275 
  CD209 MUTATED CD209 WILD-TYPE 
              5             275 
[1] "FBN3 MUTATION ANALYSIS"
[1] 3
  FBN3 MUTATED FBN3 WILD-TYPE 
            11            269 
  FBN3 MUTATED FBN3 WILD-TYPE 
            11            269 
[1] "MMP13 MUTATION ANALYSIS"
[1] 3
  MMP13 MUTATED MMP13 WILD-TYPE 
              5             275 
  MMP13 MUTATED MMP13 WILD-TYPE 
              5             275 
[1] "TCF12 MUTATION ANALYSIS"
[1] 3
  TCF12 MUTATED TCF12 WILD-TYPE 
              4             276 
  TCF12 MUTATED TCF12 WILD-TYPE 
              4             276 
[1] "LZTR1 MUTATION ANALYSIS"
[1] 3
  LZTR1 MUTATED LZTR1 WILD-TYPE 
             10             270 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
             10             270 
[1] "ZDHHC4 MUTATION ANALYSIS"
[1] 3
  ZDHHC4 MUTATED ZDHHC4 WILD-TYPE 
               3              277 
  ZDHHC4 MUTATED ZDHHC4 WILD-TYPE 
               3              277 
[1] "IL18RAP MUTATION ANALYSIS"
[1] 3
  IL18RAP MUTATED IL18RAP WILD-TYPE 
                6               274 
  IL18RAP MUTATED IL18RAP WILD-TYPE 
                6               274 
[1] "ODF4 MUTATION ANALYSIS"
[1] 3
  ODF4 MUTATED ODF4 WILD-TYPE 
             3            277 
  ODF4 MUTATED ODF4 WILD-TYPE 
             3            277 
[1] "KEL MUTATION ANALYSIS"
[1] 3
  KEL MUTATED KEL WILD-TYPE 
           15           265 
  KEL MUTATED KEL WILD-TYPE 
           15           265 
[1] "TESK1 MUTATION ANALYSIS"
[1] 3
  TESK1 MUTATED TESK1 WILD-TYPE 
              3             277 
  TESK1 MUTATED TESK1 WILD-TYPE 
              3             277 
[1] "MUC17 MUTATION ANALYSIS"
[1] 3
  MUC17 MUTATED MUC17 WILD-TYPE 
             22             258 
  MUC17 MUTATED MUC17 WILD-TYPE 
             22             258 
[1] "FAM126B MUTATION ANALYSIS"
[1] 3
  FAM126B MUTATED FAM126B WILD-TYPE 
                4               276 
  FAM126B MUTATED FAM126B WILD-TYPE 
                4               276 
[1] "DDX5 MUTATION ANALYSIS"
[1] 3
  DDX5 MUTATED DDX5 WILD-TYPE 
             4            276 
  DDX5 MUTATED DDX5 WILD-TYPE 
             4            276 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "GENDER"                              
 [7] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
 [8] "RADIATION_THERAPY"                   
 [9] "KARNOFSKY_PERFORMANCE_SCORE"         
[10] "HISTOLOGICAL_TYPE"                   
[11] "RACE"                                
[12] "ETHNICITY"                           

Input Data has 12 rows and 280 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=193,	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=56,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 8:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 10:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 280 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "GENDER"                     
[3] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
[5] "HISTOLOGICAL_TYPE"           "RACE"                       
[7] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=59, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=9, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  TP53 MUTATED    24  56
  TP53 WILD-TYPE  35 162
  TP53 MUTATED TP53 WILD-TYPE 
            80            197 
  TP53 MUTATED TP53 WILD-TYPE 
            56            162 
$`TP53 MUTATED`
TCGA-06-5408 TCGA-06-5417 TCGA-06-5858 TCGA-06-6698 TCGA-06-6701 TCGA-14-0740 
       11.74         5.10         6.15         4.77         4.96        11.97 
TCGA-14-1456 TCGA-14-1825 TCGA-14-4157 TCGA-19-1390 TCGA-19-2623 TCGA-19-2625 
       40.96         7.63         3.42        25.38         7.53         4.08 
TCGA-19-2629 TCGA-26-5136 TCGA-27-1830 TCGA-27-1835 TCGA-27-1836 TCGA-27-1838 
       24.23        18.97         5.06        21.30        30.05        11.51 
TCGA-27-2519 TCGA-27-2521 TCGA-28-1753 TCGA-28-2509 TCGA-32-1970 TCGA-32-2491 
       18.08        16.77         1.22         4.77        15.39        12.23 
TCGA-32-2634 TCGA-32-4208 TCGA-32-4210 TCGA-41-2575 TCGA-41-5651 TCGA-74-6573 
       22.78        21.14         3.72         9.53        15.12         3.45 
TCGA-76-4925 TCGA-76-4929 TCGA-76-4934 TCGA-76-6193 TCGA-76-6286 TCGA-76-6662 
        4.80         3.65         2.53         2.70        20.98        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-02-0003 TCGA-02-0033 TCGA-02-0055 TCGA-02-2483 
       18.64        36.20         4.73         2.83         2.50        15.32 
TCGA-02-2485 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0184 TCGA-06-0188 
       15.45        22.72        33.67        12.95        69.90        44.58 
TCGA-06-0189 TCGA-06-0195 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0644 
       15.42         7.40        13.64        13.32        48.69        12.62 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0875 TCGA-06-0876 TCGA-06-2558 TCGA-06-2559 
       26.40        46.88        43.46        46.19        12.49         4.93 
TCGA-06-2563 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6694 
       30.64         4.37         0.43        31.50         7.79         7.36 
TCGA-12-0618 TCGA-12-0619 TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-15-1444 
       12.99        34.92         1.35         5.39        28.93        50.53 
TCGA-16-0846 TCGA-26-1442 TCGA-26-5133 TCGA-28-5207 TCGA-28-5215 TCGA-28-5216 
        3.91        31.33        14.86        11.28        11.01        13.64 
TCGA-28-5219 TCGA-76-6283 
       22.68         5.42 

$`TP53 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        1.48        15.32         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 
        8.98         8.55         2.73         3.75         4.57         5.23 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 TCGA-06-6700 TCGA-12-0615 TCGA-12-1597 
        8.32        12.85         1.55         4.77        15.35        22.19 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       15.22        10.95        34.92        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 
        2.04         0.95        23.05        13.78         2.89         1.38 
TCGA-14-1450 TCGA-14-1823 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-16-1045 
       58.78        17.85         7.17        17.49         0.39        29.03 
TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 TCGA-19-2624 TCGA-19-2631 TCGA-19-4068 
        5.06         9.67         4.87         0.16         7.00         4.50 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 
        1.78        14.07        16.80        14.96        13.87         9.40 
TCGA-26-5135 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1837 
        8.88        16.60         9.86        24.23        40.54        14.04 
TCGA-27-2518 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       24.76        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1747 TCGA-28-2502 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        2.53         0.66         0.10        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 
       12.69        16.93        20.78        15.02        15.95         8.84 
TCGA-32-2638 TCGA-32-4209 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       25.18        20.32        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
        0.85        13.35         8.94         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-6646 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 
        0.20        12.46        20.91         4.34        14.33         7.50 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4931 TCGA-76-4932 TCGA-76-4935 
        4.54        17.59         3.09         9.17        47.93        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6282 TCGA-76-6285 TCGA-76-6656 TCGA-76-6657 
       16.70         3.29        17.06         8.35         4.83         5.03 
TCGA-76-6661 TCGA-06-0209 TCGA-02-0047 TCGA-02-2470 TCGA-02-2486 TCGA-06-0119 
       23.90         7.63        14.73        12.92        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 
        6.15        20.38         6.94        25.35        26.70        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 
        0.20        10.29         2.20         2.33        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 
       13.94        10.45         3.19        10.82        10.65         5.85 
TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 
       11.41        19.66         3.29         4.47         3.22        88.14 
TCGA-06-0185 TCGA-06-0192 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
       73.84        38.96         0.53        15.02        24.16         0.72 
TCGA-06-0240 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       20.42         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0878 
       14.20         7.86         2.70         2.70         0.92         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-2557 
       40.41        16.57        20.78        26.76        13.61         1.08 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2564 TCGA-06-2565 TCGA-06-6390 TCGA-06-6693 
       17.65        12.56         5.95        16.64         5.39       120.56 
TCGA-08-0386 TCGA-12-0616 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 
       18.02        14.73        26.66         3.65        10.62         2.24 
TCGA-14-0789 TCGA-14-1043 TCGA-15-0742 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 
       11.24         0.79        13.78         5.49         1.58         7.92 
TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 TCGA-28-5209 
        2.33         7.30         5.26        14.93        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5218 TCGA-28-5220 TCGA-28-6450 
       11.77        31.27        23.44         5.16        12.76         5.42 
TCGA-76-6280 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       11.38         3.75         1.61        17.72        26.30 

  TP53 MUTATED TP53 WILD-TYPE 
          0.43           0.10 
  TP53 MUTATED TP53 WILD-TYPE 
         69.90         120.56 
  TP53 MUTATED TP53 WILD-TYPE 
         12.97          10.65 
[1] "0.4 - 69.9 (13.0)"  "0.1 - 120.6 (10.7)"
[1] "hr=" "1.6"
D1V2, continuous
D1V3, binary
                cls
clus               0   1
  TP53 MUTATED    32  48
  TP53 WILD-TYPE  69 131
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     32   48
  TP53 WILD-TYPE   69  131
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           32             69
  MALE             48            131
[1] 2 2
[1] FALSE
D1V4, binary
                cls
clus               0   1
  TP53 MUTATED     8  66
  TP53 WILD-TYPE  38 151
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      8   66
  TP53 WILD-TYPE   38  151
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO             8             38
  YES           66            151
[1] 2 2
[1] FALSE
D1V5, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  TP53 MUTATED                               2                   0
  TP53 WILD-TYPE                             9                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  TP53 MUTATED                                78
  TP53 WILD-TYPE                             187
D1V6, multiclass
                                 clus
vv                                TP53 MUTATED TP53 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              2              9
  TREATED PRIMARY GBM                        0              4
  UNTREATED PRIMARY (DE NOVO) GBM           78            187
[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"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       2                         6    70
  TP53 WILD-TYPE     3                        11   182
D1V7, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                2              3
  BLACK OR AFRICAN AMERICAN            6             11
  WHITE                               70            182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
                cls
clus               0   1
  TP53 MUTATED     1  62
  TP53 WILD-TYPE   2 160
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1   62
  TP53 WILD-TYPE    2  160
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           62            160
[1] 2 2
[1] FALSE

Clustering(2) Variable = PIK3R1 MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2                0   1
  PIK3R1 MUTATED     7  24
  PIK3R1 WILD-TYPE  52 194
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              31              246 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              24              194 
$`PIK3R1 MUTATED`
TCGA-06-6388 TCGA-06-6695 TCGA-14-0790 TCGA-14-0862 TCGA-14-1456 TCGA-19-2629 
        5.23         8.32        13.78         2.89        40.96        24.23 
TCGA-19-5947 TCGA-19-5951 TCGA-19-5955 TCGA-19-5958 TCGA-32-1991 TCGA-32-2634 
        6.64         8.02         1.78        14.07        16.93        22.78 
TCGA-41-3915 TCGA-74-6573 TCGA-74-6575 TCGA-76-4927 TCGA-76-4929 TCGA-76-6656 
       11.84         3.45        20.91        17.59         3.65         4.83 
TCGA-76-6657 TCGA-76-6662 TCGA-02-0003 TCGA-06-0128 TCGA-06-0129 TCGA-06-0750 
        5.03        34.45         4.73        22.72        33.67         0.92 
TCGA-06-2562 TCGA-12-0688 TCGA-15-1444 TCGA-26-5139 TCGA-26-6174 TCGA-28-2513 
       12.56        26.66        50.53         1.58         2.33         7.30 
TCGA-76-6280 
       11.38 

$`PIK3R1 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        6.15         4.57        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
        4.96        15.35        22.19        15.22        10.95        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 
       14.53        14.93         3.22         2.04        11.97         0.95 
TCGA-14-0786 TCGA-14-1395 TCGA-14-1450 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 
       23.05         1.38        58.78        17.85         7.63         7.17 
TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 
       17.49         0.39         3.42        29.03        25.38         5.06 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 
        9.67         4.87         7.53         0.16         4.08         7.00 
TCGA-19-4068 TCGA-19-5950 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5959 
        4.50        17.19        18.90         4.73        12.10        16.80 
TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 
       14.96        13.87         9.40         8.88        18.97         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        18.08        16.77        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 
        7.59         2.86        14.40        15.78         2.53         1.22 
TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 
        0.66         4.77        15.39         0.10        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
        4.67        12.69        12.23        20.78        15.02        15.95 
TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 
        8.84        25.18        21.14        20.32         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        9.53         0.99         4.44         0.20        15.12        12.46 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 
        4.34        14.33         7.50         4.80         4.54         3.09 
TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        9.17        47.93         2.53        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6661 TCGA-76-6663 
        2.70        17.06         8.35        20.98        23.90        18.64 
TCGA-76-6664 TCGA-06-0209 TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 
       36.20         7.63         2.83        14.73         2.50        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0126 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 
        6.94        12.95        25.35        26.70        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.29         2.20         2.33        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 
       10.45         3.19        10.82        10.65         5.85        11.41 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 TCGA-06-0184 
       19.66         3.29         4.47         3.22        88.14        69.90 
TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0213 
       73.84        44.58        15.42        38.96         7.40         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       15.02        24.16         0.72        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       48.69        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        2.70        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       20.78        26.76        13.61         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 
       17.65        30.64         5.95        16.64         4.37         0.43 
TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 
       31.50         7.79         5.39       120.56         7.36        18.02 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 
       14.73        12.99        34.92         3.65        10.62         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 
       11.24         1.35         5.39        28.93         0.79        13.78 
TCGA-16-0846 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-6173 TCGA-28-2514 
        3.91        31.33        14.86         5.49         7.92         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        12.76 
TCGA-28-6450 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        5.42         5.42         3.75         1.61        17.72        26.30 

  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
            0.92             0.10 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           50.53           120.56 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
          11.380           11.625 
[1] "0.9 - 50.5 (11.4)"  "0.1 - 120.6 (11.6)"
[1] "hr=" "1.1"
D2V2, continuous
D2V3, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     9  23
  PIK3R1 WILD-TYPE  92 156
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      9   23
  PIK3R1 WILD-TYPE   92  156
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  FEMALE              9               92
  MALE               23              156
[1] 2 2
[1] FALSE
D2V4, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     5  25
  PIK3R1 WILD-TYPE  41 192
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      5   25
  PIK3R1 WILD-TYPE   41  192
     clus
vv    PIK3R1 MUTATED PIK3R1 WILD-TYPE
  NO               5               41
  YES             25              192
[1] 2 2
[1] FALSE
D2V5, continuous
                  vv
clus               GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  PIK3R1 MUTATED                               1                   0
  PIK3R1 WILD-TYPE                            10                   4
                  vv
clus               UNTREATED PRIMARY (DE NOVO) GBM
  PIK3R1 MUTATED                                31
  PIK3R1 WILD-TYPE                             234
D2V6, multiclass
                                 clus
vv                                PIK3R1 MUTATED PIK3R1 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                1               10
  TREATED PRIMARY GBM                          0                4
  UNTREATED PRIMARY (DE NOVO) GBM             31              234
[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"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3R1 MUTATED       1                         2    27
  PIK3R1 WILD-TYPE     4                        15   225
D2V7, multiclass
                           clus
vv                          PIK3R1 MUTATED PIK3R1 WILD-TYPE
  ASIAN                                  1                4
  BLACK OR AFRICAN AMERICAN              2               15
  WHITE                                 27              225
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     0  26
  PIK3R1 WILD-TYPE   3 196
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      0   26
  PIK3R1 WILD-TYPE    3  196
                        clus
vv                       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             26              196
[1] 2 2
[1] FALSE

Clustering(3) Variable = RB1 MUTATION ANALYSIS
D3V1, survival
               sevent
clus2             0   1
  RB1 MUTATED     7  17
  RB1 WILD-TYPE  52 201
  RB1 MUTATED RB1 WILD-TYPE 
           24           253 
  RB1 MUTATED RB1 WILD-TYPE 
           17           201 
$`RB1 MUTATED`
TCGA-06-5858 TCGA-06-6698 TCGA-19-2623 TCGA-19-2625 TCGA-26-5132 TCGA-27-2524 
        6.15         4.77         7.53         4.08         9.40         7.59 
TCGA-32-1970 TCGA-32-2491 TCGA-32-2632 TCGA-32-2634 TCGA-32-4213 TCGA-76-6286 
       15.39        12.23         8.84        22.78        19.86        20.98 
TCGA-76-6662 TCGA-76-6663 TCGA-02-0033 TCGA-06-0130 TCGA-06-0140 TCGA-06-0184 
       34.45        18.64         2.83        12.95         0.20        69.90 
TCGA-06-0188 TCGA-06-0195 TCGA-06-0213 TCGA-06-0939 TCGA-76-6283 TCGA-81-5911 
       44.58         7.40         0.53        26.76         5.42        17.72 

$`RB1 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 TCGA-06-6700 
        4.57         5.23         8.32        12.85         1.55         4.77 
TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
        4.96        15.35        22.19        15.22        10.95        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 
       14.53        14.93         3.22         2.04        11.97         0.95 
TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 
       23.05        13.78         2.89         1.38        58.78        40.96 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 
       17.85         7.63         7.17        17.49         0.39         3.42 
TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 TCGA-19-2624 
       29.03        25.38         5.06         9.67         4.87         0.16 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       24.23         7.00         4.50         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 
       18.90         4.73        12.10         1.78        14.07        16.80 
TCGA-19-5960 TCGA-26-1439 TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 
       14.96        13.87         8.88        18.97         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        24.23        40.54        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2526 
       11.51        24.76        18.08        16.77        16.08         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 
       14.40        15.78         2.53         1.22         0.66         4.77 
TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 
        0.10        19.50         1.18         4.67        12.69        16.93 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 
       20.78        15.02        15.95        25.18        21.14        20.32 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
        3.72        12.59        10.85        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
        8.94         9.53         0.99         4.44        11.84         0.20 
TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
       15.12        12.46         3.45        20.91         4.34        14.33 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 
        7.50         4.80         4.54        17.59         3.09         3.65 
TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        9.17        47.93         2.53        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
        2.70        17.06         8.35         4.83         5.03        23.90 
TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 
       36.20         7.63         4.73        14.73         2.50        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 
        6.94        22.72        33.67        25.35        26.70        11.90 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.29         2.20         2.33        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 
       10.45         3.19        10.82        10.65         5.85        11.41 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 TCGA-06-0185 
       19.66         3.29         4.47         3.22        88.14        73.84 
TCGA-06-0189 TCGA-06-0192 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
       15.42        38.96        15.02        24.16         0.72        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
       13.32        20.42        48.69        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-1804 TCGA-06-2557 
        7.17        40.41        16.57        20.78        13.61         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 
       16.64         4.37         0.43        31.50         7.79         5.39 
TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
      120.56         7.36        18.02        14.73        12.99        34.92 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 
       26.66         3.65        10.62         2.24        11.24         1.35 
TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-16-0846 
        5.39        28.93         0.79        13.78        50.53         3.91 
TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
       31.33        14.86         5.49         1.58         7.92         2.33 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        23.44        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6660 TCGA-81-5910 
       22.68        12.76         5.42        11.38         3.75         1.61 
TCGA-87-5896 
       26.30 

  RB1 MUTATED RB1 WILD-TYPE 
          0.2           0.1 
  RB1 MUTATED RB1 WILD-TYPE 
        69.90        120.56 
  RB1 MUTATED RB1 WILD-TYPE 
       10.815        11.510 
[1] "0.2 - 69.9 (10.8)"  "0.1 - 120.6 (11.5)"
[1] "hr=" "1.3"
D3V2, continuous
D3V3, binary
               cls
clus              0   1
  RB1 MUTATED     8  16
  RB1 WILD-TYPE  93 163
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      8   16
  RB1 WILD-TYPE   93  163
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE           8            93
  MALE            16           163
[1] 2 2
[1] FALSE
D3V4, binary
               cls
clus              0   1
  RB1 MUTATED     4  18
  RB1 WILD-TYPE  42 199
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      4   18
  RB1 WILD-TYPE   42  199
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO            4            42
  YES          18           199
[1] 2 2
[1] FALSE
D3V5, continuous
               vv
clus            GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  RB1 MUTATED                               2                   0
  RB1 WILD-TYPE                             9                   4
               vv
clus            UNTREATED PRIMARY (DE NOVO) GBM
  RB1 MUTATED                                22
  RB1 WILD-TYPE                             243
D3V6, multiclass
                                 clus
vv                                RB1 MUTATED RB1 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)             2             9
  TREATED PRIMARY GBM                       0             4
  UNTREATED PRIMARY (DE NOVO) GBM          22           243
[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"
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED       0                         0    24
  RB1 WILD-TYPE     5                        17   228
D3V7, multiclass
                           clus
vv                          RB1 MUTATED RB1 WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0            17
  WHITE                              24           228
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
               cls
clus              0   1
  RB1 MUTATED     0  20
  RB1 WILD-TYPE   3 202
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0   20
  RB1 WILD-TYPE    3  202
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          20           202
[1] 2 2
[1] FALSE

Clustering(4) Variable = NF1 MUTATION ANALYSIS
D4V1, survival
               sevent
clus2             0   1
  NF1 MUTATED     5  24
  NF1 WILD-TYPE  54 194
  NF1 MUTATED NF1 WILD-TYPE 
           29           248 
  NF1 MUTATED NF1 WILD-TYPE 
           24           194 
$`NF1 MUTATED`
TCGA-06-5410 TCGA-06-5412 TCGA-06-6698 TCGA-19-2620 TCGA-19-5953 TCGA-28-2502 
        3.55         4.54         4.77         4.87         4.73         0.66 
TCGA-32-1980 TCGA-32-1986 TCGA-32-2494 TCGA-41-3392 TCGA-41-4097 TCGA-41-6646 
        1.18        12.69        20.78         0.99         0.20        12.46 
TCGA-74-6575 TCGA-76-6657 TCGA-76-6663 TCGA-02-0033 TCGA-06-0119 TCGA-06-0124 
       20.91         5.03        18.64         2.83         2.70        20.38 
TCGA-06-0184 TCGA-06-0192 TCGA-06-0214 TCGA-06-2562 TCGA-06-2569 TCGA-14-0789 
       69.90        38.96        15.02        12.56         0.43        11.24 
TCGA-14-0871 TCGA-14-1043 TCGA-26-5133 TCGA-28-5208 TCGA-28-6450 
       28.93         0.79        14.86        17.88         5.42 

$`NF1 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5411 TCGA-06-5413 TCGA-06-5414 
        1.48        15.32        11.74         8.35         8.81         8.98 
TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.55         5.10         2.73         3.75         6.15         4.57 
TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        5.23         8.32        12.85         1.55         4.77         4.96 
TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 
       15.35        22.19        15.22        10.95        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 
       14.93         3.22         2.04        11.97         0.95        23.05 
TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 
       13.78         2.89         1.38        58.78        40.96        17.85 
TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 TCGA-16-1045 
        7.63         7.17        17.49         0.39         3.42        29.03 
TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
       25.38         5.06         9.67         7.53         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       24.23         7.00         4.50         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
       18.90        12.10         1.78        14.07        16.80        14.96 
TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 
       13.87         9.40         8.88        18.97         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        24.23        40.54        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 
       11.51        24.76        18.08        16.77        16.08         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2509 
        2.86        14.40        15.78         2.53         1.22         4.77 
TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1982 TCGA-32-1991 TCGA-32-2491 
       15.39         0.10        19.50         4.67        16.93        12.23 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.02        15.95         8.84        22.78        25.18        21.14 
TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       20.32         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3393 TCGA-41-3915 
        0.85        13.35         8.94         9.53         4.44        11.84 
TCGA-41-5651 TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 
       15.12         3.45         4.34        14.33         7.50         4.80 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 
        4.54        17.59         3.09         3.65         9.17        47.93 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        2.53        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6661 TCGA-76-6662 TCGA-76-6664 
        8.35        20.98         4.83        23.90        34.45        36.20 
TCGA-06-0209 TCGA-02-0003 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 
        7.63         4.73        14.73         2.50        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0122 TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 
       15.45        20.32         6.15         6.94        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       12.95        25.35        26.70        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        2.20         2.33        46.59        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 TCGA-06-0168 
        3.19        10.82        10.65         5.85        11.41        19.66 
TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 TCGA-06-0185 TCGA-06-0188 
        3.29         4.47         3.22        88.14        73.84        44.58 
TCGA-06-0189 TCGA-06-0195 TCGA-06-0213 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
       15.42         7.40         0.53        24.16         0.72        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
       13.32        20.42        48.69        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 
        7.17        40.41        16.57        20.78        26.76        13.61 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2563 TCGA-06-2564 
        1.08        12.49         4.93        17.65        30.64         5.95 
TCGA-06-2565 TCGA-06-2567 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 
       16.64         4.37        31.50         7.79         5.39       120.56 
TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 
        7.36        18.02        14.73        12.99        34.92        26.66 
TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0813 TCGA-14-0817 TCGA-15-0742 
        3.65        10.62         2.24         1.35         5.39        13.78 
TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 
       50.53         3.91        31.33         5.49         1.58         7.92 
TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5209 
        2.33         7.30         5.26        14.93        11.28        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        23.44        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 
       22.68        12.76        11.38         5.42         3.75         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

  NF1 MUTATED NF1 WILD-TYPE 
          0.2           0.1 
  NF1 MUTATED NF1 WILD-TYPE 
        69.90        120.56 
  NF1 MUTATED NF1 WILD-TYPE 
        5.420        11.755 
[1] "0.2 - 69.9 (5.4)"   "0.1 - 120.6 (11.8)"
[1] "hr=" "1.3"
D4V2, continuous
D4V3, binary
               cls
clus              0   1
  NF1 MUTATED    11  18
  NF1 WILD-TYPE  90 161
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     11   18
  NF1 WILD-TYPE   90  161
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE          11            90
  MALE            18           161
[1] 2 2
[1] FALSE
D4V4, binary
               cls
clus              0   1
  NF1 MUTATED     6  21
  NF1 WILD-TYPE  40 196
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      6   21
  NF1 WILD-TYPE   40  196
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO            6            40
  YES          21           196
[1] 2 2
[1] FALSE
D4V5, continuous
               vv
clus            GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  NF1 MUTATED                               1                   0
  NF1 WILD-TYPE                            10                   4
               vv
clus            UNTREATED PRIMARY (DE NOVO) GBM
  NF1 MUTATED                                28
  NF1 WILD-TYPE                             237
D4V6, multiclass
                                 clus
vv                                NF1 MUTATED NF1 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)             1            10
  TREATED PRIMARY GBM                       0             4
  UNTREATED PRIMARY (DE NOVO) GBM          28           237
[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"
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED       0                         1    27
  NF1 WILD-TYPE     5                        16   225
D4V7, multiclass
                           clus
vv                          NF1 MUTATED NF1 WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           1            16
  WHITE                              27           225
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
               cls
clus              0   1
  NF1 MUTATED     0  21
  NF1 WILD-TYPE   3 201
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      0   21
  NF1 WILD-TYPE    3  201
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          21           201
[1] 2 2
[1] FALSE

Clustering(5) Variable = PTEN MUTATION ANALYSIS
D5V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    17  68
  PTEN WILD-TYPE  42 150
  PTEN MUTATED PTEN WILD-TYPE 
            85            192 
  PTEN MUTATED PTEN WILD-TYPE 
            68            150 
$`PTEN MUTATED`
TCGA-06-5411 TCGA-06-5412 TCGA-06-5418 TCGA-06-5858 TCGA-12-1597 TCGA-12-3649 
        8.35         4.54         2.73         6.15        22.19        15.22 
TCGA-14-0781 TCGA-14-1395 TCGA-16-1045 TCGA-19-2625 TCGA-19-5952 TCGA-19-5953 
        0.95         1.38        29.03         4.08        18.90         4.73 
TCGA-19-5955 TCGA-19-5959 TCGA-26-5132 TCGA-27-1834 TCGA-27-1837 TCGA-27-1838 
        1.78        16.80         9.40        40.54        14.04        11.51 
TCGA-27-2519 TCGA-27-2524 TCGA-27-2526 TCGA-28-1753 TCGA-28-2502 TCGA-32-1977 
       18.08         7.59         2.86         1.22         0.66         0.10 
TCGA-32-1982 TCGA-32-1991 TCGA-32-2495 TCGA-32-2634 TCGA-32-4210 TCGA-32-4213 
        4.67        16.93        15.02        22.78         3.72        19.86 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2573 TCGA-41-3915 TCGA-41-4097 TCGA-74-6577 
       19.23         0.85         8.94        11.84         0.20         4.34 
TCGA-76-4925 TCGA-76-4927 TCGA-76-4931 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        4.80        17.59         9.17         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6286 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6664 
        3.29        20.98         5.03        23.90        34.45        36.20 
TCGA-02-0055 TCGA-02-2470 TCGA-06-0124 TCGA-06-0155 TCGA-06-0157 TCGA-06-0166 
        2.50        12.92        20.38        10.45         3.19         5.85 
TCGA-06-0168 TCGA-06-0184 TCGA-06-0188 TCGA-06-0192 TCGA-06-0195 TCGA-06-0213 
       19.66        69.90        44.58        38.96         7.40         0.53 
TCGA-06-0216 TCGA-06-0644 TCGA-06-0649 TCGA-06-0743 TCGA-06-0749 TCGA-06-0875 
       24.16        12.62         2.10        26.40         2.70        43.46 
TCGA-06-0876 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-2558 
       46.19        16.57        20.78        26.76        13.61        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2565 TCGA-12-0618 TCGA-14-0813 TCGA-16-0846 
        4.93        17.65        16.64        12.99         1.35         3.91 
TCGA-26-6174 TCGA-28-2513 TCGA-28-5209 TCGA-28-5216 TCGA-76-6283 TCGA-81-5910 
        2.33         7.30        14.53        13.64         5.42         1.61 
TCGA-81-5911 
       17.72 

$`PTEN WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5413 TCGA-06-5414 
        1.48        15.32        11.74         3.55         8.81         8.98 
TCGA-06-5415 TCGA-06-5417 TCGA-06-5856 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 
        8.55         5.10         3.75         4.57         5.23         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 
       12.85         4.77         1.55         4.77         4.96        15.35 
TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0740 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1450 TCGA-14-1456 
       11.97        23.05        13.78         2.89        58.78        40.96 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 
       17.85         7.63         7.17        17.49         0.39         3.42 
TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 
       25.38         5.06         9.67         4.87         7.53         0.16 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       24.23         7.00         4.50         6.64        17.19         8.02 
TCGA-19-5954 TCGA-19-5958 TCGA-19-5960 TCGA-26-1439 TCGA-26-5135 TCGA-26-5136 
       12.10        14.07        14.96        13.87         8.88        18.97 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1835 TCGA-27-1836 
        5.06        16.60         9.86        24.23        21.30        30.05 
TCGA-27-2518 TCGA-27-2521 TCGA-27-2523 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 
       24.76        16.77        16.08        14.40        15.78         2.53 
TCGA-28-2509 TCGA-32-1970 TCGA-32-1979 TCGA-32-1980 TCGA-32-1986 TCGA-32-2491 
        4.77        15.39        19.50         1.18        12.69        12.23 
TCGA-32-2494 TCGA-32-2615 TCGA-32-2632 TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 
       20.78        15.95         8.84        25.18        21.14        20.32 
TCGA-32-4211 TCGA-32-4719 TCGA-41-2572 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
       12.59        10.85        13.35         9.53         0.99         4.44 
TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6578 TCGA-74-6584 
       15.12        12.46         3.45        20.91        14.33         7.50 
TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4932 TCGA-76-6193 TCGA-76-6282 
        4.54         3.09         3.65        47.93         2.70        17.06 
TCGA-76-6285 TCGA-76-6656 TCGA-76-6663 TCGA-06-0209 TCGA-02-0003 TCGA-02-0033 
        8.35         4.83        18.64         7.63         4.73         2.83 
TCGA-02-0047 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       14.73        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 
        6.94        22.72        33.67        12.95        25.35        26.70 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 
       11.90         0.20        10.29         2.20         2.33        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0158 TCGA-06-0165 TCGA-06-0167 TCGA-06-0169 
       12.33        13.94        10.82        10.65        11.41         3.29 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 TCGA-06-0185 TCGA-06-0189 TCGA-06-0214 
        4.47         3.22        88.14        73.84        15.42        15.02 
TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0645 
        0.72        13.64        13.32        20.42        48.69         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 
        5.75         9.80        23.57        14.20        46.88         7.86 
TCGA-06-0747 TCGA-06-0750 TCGA-06-0878 TCGA-06-0879 TCGA-06-2557 TCGA-06-2562 
        2.70         0.92         7.17        40.41         1.08        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 
       30.64         5.95         4.37         0.43        31.50         7.79 
TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0619 
        5.39       120.56         7.36        18.02        14.73        34.92 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0817 
       26.66         3.65        10.62         2.24        11.24         5.39 
TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-26-1442 TCGA-26-5133 
       28.93         0.79        13.78        50.53        31.33        14.86 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        5.49         1.58         7.92         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 
       17.88        11.77        31.27        23.44        11.01         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6660 TCGA-87-5896 
       22.68        12.76         5.42        11.38         3.75        26.30 

  PTEN MUTATED PTEN WILD-TYPE 
          0.10           0.16 
  PTEN MUTATED PTEN WILD-TYPE 
         69.90         120.56 
  PTEN MUTATED PTEN WILD-TYPE 
        11.840         11.395 
[1] "0.1 - 69.9 (11.8)"  "0.2 - 120.6 (11.4)"
[1] "hr=" "1"  
D5V2, continuous
D5V3, binary
                cls
clus               0   1
  PTEN MUTATED    34  52
  PTEN WILD-TYPE  67 127
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     34   52
  PTEN WILD-TYPE   67  127
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE           34             67
  MALE             52            127
[1] 2 2
[1] FALSE
D5V4, binary
                cls
clus               0   1
  PTEN MUTATED    19  61
  PTEN WILD-TYPE  27 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     19   61
  PTEN WILD-TYPE   27  156
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO            19             27
  YES           61            156
[1] 2 2
[1] FALSE
D5V5, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  PTEN MUTATED                               1                   2
  PTEN WILD-TYPE                            10                   2
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  PTEN MUTATED                                83
  PTEN WILD-TYPE                             182
D5V6, multiclass
                                 clus
vv                                PTEN MUTATED PTEN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              1             10
  TREATED PRIMARY GBM                        2              2
  UNTREATED PRIMARY (DE NOVO) GBM           83            182
[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"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       1                         5    79
  PTEN WILD-TYPE     4                        12   173
D5V7, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                1              4
  BLACK OR AFRICAN AMERICAN            5             12
  WHITE                               79            173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                cls
clus               0   1
  PTEN MUTATED     2  68
  PTEN WILD-TYPE   1 154
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      2   68
  PTEN WILD-TYPE    1  154
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                2              1
  NOT HISPANIC OR LATINO           68            154
[1] 2 2
[1] FALSE

Clustering(6) Variable = IDH1 MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  IDH1 MUTATED     9   5
  IDH1 WILD-TYPE  50 213
  IDH1 MUTATED IDH1 WILD-TYPE 
            14            263 
  IDH1 MUTATED IDH1 WILD-TYPE 
             5            213 
$`IDH1 MUTATED`
TCGA-06-5417 TCGA-06-6701 TCGA-14-1456 TCGA-14-4157 TCGA-19-2629 TCGA-27-2521 
        5.10         4.96        40.96         3.42        24.23        16.77 
TCGA-32-4208 TCGA-02-2483 TCGA-06-0128 TCGA-06-0129 TCGA-06-2570 TCGA-06-6389 
       21.14        15.32        22.72        33.67        31.50         7.79 
TCGA-15-1444 TCGA-26-1442 
       50.53        31.33 

$`IDH1 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.81         8.98         8.55         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
        4.77        15.35        22.19        15.22        10.95        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 
       14.53        14.93         3.22         2.04        11.97         0.95 
TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 TCGA-14-1823 
       23.05        13.78         2.89         1.38        58.78        17.85 
TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-16-1045 TCGA-19-1390 
        7.63         7.17        17.49         0.39        29.03        25.38 
TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        5.06         9.67         4.87         7.53         0.16         4.08 
TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         4.50         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        4.73        12.10         1.78        14.07        16.80        14.96 
TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 
       13.87         9.40         8.88        18.97         5.06        16.60 
TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 
        9.86        24.23        40.54        21.30        30.05        14.04 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       11.51        24.76        18.08        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 
       14.40        15.78         2.53         1.22         0.66         4.77 
TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
       15.39         0.10        19.50         1.18         4.67        12.69 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 
       16.93        12.23        20.78        15.02        15.95         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       22.78        25.18        20.32         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 
        3.45        20.91         4.34        14.33         7.50         4.80 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 
        4.54        17.59         3.09         3.65         9.17        47.93 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        2.53        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 
       18.64        36.20         7.63         4.73         2.83        14.73 
TCGA-02-0055 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
        2.50        12.92        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0126 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 
       20.38         6.94        12.95        25.35        26.70        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 
        0.20        10.29         2.20         2.33        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 
       13.94        10.45         3.19        10.82        10.65         5.85 
TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 
       11.41        19.66         3.29         4.47         3.22        88.14 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 
       69.90        73.84        44.58        15.42        38.96         7.40 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 
        0.53        15.02        24.16         0.72        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
       20.42        48.69        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.10        23.57        14.20        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 
        2.70         2.70         0.92        43.46        46.19         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-2557 
       40.41        16.57        20.78        26.76        13.61         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 
       16.64         4.37         0.43         5.39       120.56         7.36 
TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 
       18.02        14.73        12.99        34.92        26.66         3.65 
TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 
       10.62         2.24        11.24         1.35         5.39        28.93 
TCGA-14-1043 TCGA-15-0742 TCGA-16-0846 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 
        0.79        13.78         3.91        14.86         5.49         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        7.92         2.33         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 
       13.64         5.16        22.68        12.76         5.42        11.38 
TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        5.42         3.75         1.61        17.72        26.30 

  IDH1 MUTATED IDH1 WILD-TYPE 
          3.42           0.10 
  IDH1 MUTATED IDH1 WILD-TYPE 
         50.53         120.56 
  IDH1 MUTATED IDH1 WILD-TYPE 
         21.93          11.28 
[1] "3.4 - 50.5 (21.9)"  "0.1 - 120.6 (11.3)"
[1] "hr=" "4"  
D6V2, continuous
D6V3, binary
                cls
clus               0   1
  IDH1 MUTATED     3  11
  IDH1 WILD-TYPE  98 168
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      3   11
  IDH1 WILD-TYPE   98  168
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  FEMALE            3             98
  MALE             11            168
[1] 2 2
[1] FALSE
D6V4, binary
                cls
clus               0   1
  IDH1 MUTATED     0  14
  IDH1 WILD-TYPE  46 203
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      0   14
  IDH1 WILD-TYPE   46  203
     clus
vv    IDH1 MUTATED IDH1 WILD-TYPE
  NO             0             46
  YES           14            203
[1] 2 2
[1] FALSE
D6V5, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  IDH1 MUTATED                               1                   0
  IDH1 WILD-TYPE                            10                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  IDH1 MUTATED                                13
  IDH1 WILD-TYPE                             252
D6V6, multiclass
                                 clus
vv                                IDH1 MUTATED IDH1 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              1             10
  TREATED PRIMARY GBM                        0              4
  UNTREATED PRIMARY (DE NOVO) GBM           13            252
[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"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IDH1 MUTATED       2                         1    11
  IDH1 WILD-TYPE     3                        16   241
D6V7, multiclass
                           clus
vv                          IDH1 MUTATED IDH1 WILD-TYPE
  ASIAN                                2              3
  BLACK OR AFRICAN AMERICAN            1             16
  WHITE                               11            241
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                cls
clus               0   1
  IDH1 MUTATED     0  12
  IDH1 WILD-TYPE   3 210
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      0   12
  IDH1 WILD-TYPE    3  210
                        clus
vv                       IDH1 MUTATED IDH1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           12            210
[1] 2 2
[1] FALSE

Clustering(7) Variable = PIK3CA MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED     5  21
  PIK3CA WILD-TYPE  54 197
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26              251 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              21              197 
$`PIK3CA MUTATED`
TCGA-06-6391 TCGA-06-5413 TCGA-06-5417 TCGA-12-5301 TCGA-19-1790 TCGA-19-5947 
        1.48         8.81         5.10         2.04         5.06         6.64 
TCGA-19-5954 TCGA-26-5136 TCGA-27-1838 TCGA-27-2527 TCGA-32-2491 TCGA-41-2572 
       12.10        18.97        11.51        14.40        12.23        13.35 
TCGA-41-5651 TCGA-74-6578 TCGA-76-4928 TCGA-76-6193 TCGA-76-6286 TCGA-02-0033 
       15.12        14.33         3.09         2.70        20.98         2.83 
TCGA-02-0047 TCGA-02-2485 TCGA-06-0119 TCGA-06-0166 TCGA-06-0879 TCGA-06-2570 
       14.73        15.45         2.70         5.85        40.41        31.50 
TCGA-15-0742 TCGA-28-6450 
       13.78         5.42 

$`PIK3CA WILD-TYPE`
TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5414 
       15.32        11.74         3.55         8.35         4.54         8.98 
TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        8.55         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        8.32        12.85         4.77         1.55         4.77         4.96 
TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 
       15.35        22.19        15.22        10.95        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 
       14.93         3.22        11.97         0.95        23.05        13.78 
TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 
        2.89         1.38        58.78        40.96        17.85         7.63 
TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 
        7.17        17.49         0.39         3.42        29.03        25.38 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 
        9.67         4.87         7.53         0.16         4.08        24.23 
TCGA-19-2631 TCGA-19-4068 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        7.00         4.50        17.19         8.02        18.90         4.73 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 
        1.78        14.07        16.80        14.96        13.87         9.40 
TCGA-26-5135 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        8.88         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       21.30        30.05        14.04        24.76        18.08        16.77 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 
       16.08         7.59         2.86        15.78         2.53         1.22 
TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 
        0.66         4.77        15.39         0.10        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
        4.67        12.69        16.93        20.78        15.02        15.95 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 
        8.84        22.78        25.18        21.14        20.32         3.72 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2573 
       12.59        19.86        10.85        19.23         0.85         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 
        9.53         0.99         4.44        11.84         0.20        12.46 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
        3.45        20.91         4.34         7.50         4.80         4.54 
TCGA-76-4927 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 
       17.59         3.65         9.17        47.93         2.53        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6282 TCGA-76-6285 TCGA-76-6656 TCGA-76-6657 
       16.70         3.29        17.06         8.35         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 
       23.90        34.45        18.64        36.20         7.63         4.73 
TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 TCGA-02-2486 TCGA-06-0122 TCGA-06-0124 
        2.50        12.92        15.32        20.32         6.15        20.38 
TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 
        6.94        22.72        33.67        12.95        25.35        26.70 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 
       11.90         0.20        10.29         2.20         2.33        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 
       12.33        13.94        10.45         3.19        10.82        10.65 
TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 
       11.41        19.66         3.29         4.47         3.22        88.14 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 
       69.90        73.84        44.58        15.42        38.96         7.40 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 
        0.53        15.02        24.16         0.72        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
       20.42        48.69        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.10        23.57        14.20        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 
        2.70         2.70         0.92        43.46        46.19         7.17 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 
       16.57        20.78        26.76        13.61         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2567 TCGA-06-2569 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 
        4.37         0.43         7.79         5.39       120.56         7.36 
TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 
       18.02        14.73        12.99        34.92        26.66         3.65 
TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 
       10.62         2.24        11.24         1.35         5.39        28.93 
TCGA-14-1043 TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 
        0.79        50.53         3.91        31.33        14.86         5.49 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        1.58         7.92         2.33         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-76-6280 
       11.01        13.64         5.16        22.68        12.76        11.38 
TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        5.42         3.75         1.61        17.72        26.30 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            1.48             0.10 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           40.41           120.56 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          11.805           11.410 
[1] "1.5 - 40.4 (11.8)"  "0.1 - 120.6 (11.4)"
[1] "hr=" "1.3"
D7V2, continuous
D7V3, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    10  16
  PIK3CA WILD-TYPE  91 163
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     10   16
  PIK3CA WILD-TYPE   91  163
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             10               91
  MALE               16              163
[1] 2 2
[1] FALSE
D7V4, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     3  22
  PIK3CA WILD-TYPE  43 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      3   22
  PIK3CA WILD-TYPE   43  195
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO               3               43
  YES             22              195
[1] 2 2
[1] FALSE
D7V5, continuous
                  vv
clus               GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  PIK3CA MUTATED                               1                   0
  PIK3CA WILD-TYPE                            10                   4
                  vv
clus               UNTREATED PRIMARY (DE NOVO) GBM
  PIK3CA MUTATED                                25
  PIK3CA WILD-TYPE                             240
D7V6, multiclass
                                 clus
vv                                PIK3CA MUTATED PIK3CA WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                1               10
  TREATED PRIMARY GBM                          0                4
  UNTREATED PRIMARY (DE NOVO) GBM             25              240
[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"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED       0                         3    21
  PIK3CA WILD-TYPE     5                        14   231
D7V7, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              3               14
  WHITE                                 21              231
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     0  21
  PIK3CA WILD-TYPE   3 201
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      0   21
  PIK3CA WILD-TYPE    3  201
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             21              201
[1] 2 2
[1] FALSE

Clustering(8) Variable = STAG2 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2               0   1
  STAG2 MUTATED     1  11
  STAG2 WILD-TYPE  58 207
  STAG2 MUTATED STAG2 WILD-TYPE 
             12             265 
  STAG2 MUTATED STAG2 WILD-TYPE 
             11             207 
$`STAG2 MUTATED`
TCGA-06-6388 TCGA-14-2554 TCGA-19-5955 TCGA-32-5222 TCGA-41-4097 TCGA-74-6577 
        5.23        17.49         1.78        19.23         0.20         4.34 
TCGA-06-0749 TCGA-06-2561 TCGA-12-0692 TCGA-12-0821 TCGA-14-0789 TCGA-81-5910 
        2.70        17.65         3.65        10.62        11.24         1.61 

$`STAG2 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        6.15         4.57         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 
        4.77         4.96        15.35        22.19        15.22        10.95 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 
       34.92        14.53        14.93         3.22         2.04        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 
        0.95        23.05        13.78         2.89         1.38        58.78 
TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-3476 TCGA-14-4157 
       40.96        17.85         7.63         7.17         0.39         3.42 
TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 
       29.03        25.38         5.06         9.67         4.87         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 
        0.16         4.08        24.23         7.00         4.50         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5958 
       17.19         8.02        18.90         4.73        12.10        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 
       16.80        14.96        13.87         9.40         8.88        18.97 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        14.04        11.51        24.76        18.08        16.77 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 
       16.08         7.59         2.86        14.40        15.78         2.53 
TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 
        1.22         0.66         4.77        15.39         0.10        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        1.18         4.67        12.69        16.93        12.23        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.02        15.95         8.84        22.78        25.18        21.14 
TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 
       20.32         3.72        12.59        19.86        10.85         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6578 TCGA-74-6584 
       15.12        12.46         3.45        20.91        14.33         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        4.80         4.54        17.59         3.09         3.65         9.17 
TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
       47.93         2.53        36.85        16.70         3.29         2.70 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       17.06         8.35        20.98         4.83         5.03        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 TCGA-02-0033 
       34.45        18.64        36.20         7.63         4.73         2.83 
TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
       14.73         2.50        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 
        2.70         6.15        20.38         6.94        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       12.95        25.35        26.70        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        2.20         2.33        46.59        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 TCGA-06-0168 
        3.19        10.82        10.65         5.85        11.41        19.66 
TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 TCGA-06-0184 TCGA-06-0185 
        3.29         4.47         3.22        88.14        69.90        73.84 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0213 TCGA-06-0214 
       44.58        15.42        38.96         7.40         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       24.16         0.72        13.64        13.32        20.42        48.69 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.62         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0750 
       14.20        26.40        46.88         7.86         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       43.46        46.19         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 
       26.76        13.61         1.08        12.49         4.93        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
       30.64         5.95        16.64         4.37         0.43        31.50 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 
        7.79         5.39       120.56         7.36        18.02        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-14-0787 TCGA-14-0813 TCGA-14-0817 
       12.99        34.92        26.66         2.24         1.35         5.39 
TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 
       28.93         0.79        13.78        50.53         3.91        31.33 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 
       14.86         5.49         1.58         7.92         2.33         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        23.44        11.01        13.64         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5911 
       12.76         5.42        11.38         5.42         3.75        17.72 
TCGA-87-5896 
       26.30 

  STAG2 MUTATED STAG2 WILD-TYPE 
            0.2             0.1 
  STAG2 MUTATED STAG2 WILD-TYPE 
          19.23          120.56 
  STAG2 MUTATED STAG2 WILD-TYPE 
          4.785          11.840 
[1] "0.2 - 19.2 (4.8)"   "0.1 - 120.6 (11.8)"
[1] "hr=" "2.2"
D8V2, continuous
D8V3, binary
                 cls
clus                0   1
  STAG2 MUTATED     5   7
  STAG2 WILD-TYPE  96 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      5    7
  STAG2 WILD-TYPE   96  172
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  FEMALE             5              96
  MALE               7             172
[1] 2 2
[1] FALSE
D8V4, binary
                 cls
clus                0   1
  STAG2 MUTATED     4   8
  STAG2 WILD-TYPE  42 209
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      4    8
  STAG2 WILD-TYPE   42  209
     clus
vv    STAG2 MUTATED STAG2 WILD-TYPE
  NO              4              42
  YES             8             209
[1] 2 2
[1] FALSE
D8V5, continuous
                 vv
clus              GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  STAG2 MUTATED                               0                   0
  STAG2 WILD-TYPE                            11                   4
                 vv
clus              UNTREATED PRIMARY (DE NOVO) GBM
  STAG2 MUTATED                                12
  STAG2 WILD-TYPE                             253
D8V6, multiclass
                                 clus
vv                                STAG2 MUTATED STAG2 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)               0              11
  TREATED PRIMARY GBM                         0               4
  UNTREATED PRIMARY (DE NOVO) GBM            12             253
[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"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STAG2 MUTATED       0                         1    10
  STAG2 WILD-TYPE     5                        16   242
D8V7, multiclass
                           clus
vv                          STAG2 MUTATED STAG2 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             1              16
  WHITE                                10             242
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                 cls
clus                0   1
  STAG2 MUTATED     0   8
  STAG2 WILD-TYPE   3 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      0    8
  STAG2 WILD-TYPE    3  214
                        clus
vv                       STAG2 MUTATED STAG2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             8             214
[1] 2 2
[1] FALSE

Clustering(9) Variable = SLC26A3 MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  SLC26A3 MUTATED     2   5
  SLC26A3 WILD-TYPE  57 213
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
                7               270 
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
                5               213 
$`SLC26A3 MUTATED`
TCGA-32-4211 TCGA-02-0003 TCGA-06-2563 TCGA-12-0618 TCGA-15-0742 TCGA-28-5216 
       12.59         4.73        30.64        12.99        13.78        13.64 
TCGA-76-6660 
        3.75 

$`SLC26A3 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 
        1.55         4.77         4.96        15.35        22.19        15.22 
TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 
       11.97         0.95        23.05        13.78         2.89         1.38 
TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 
       58.78        40.96        17.85         7.63         7.17        17.49 
TCGA-14-3476 TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 
        0.39         3.42        29.03        25.38         5.06         9.67 
TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        4.87         7.53         0.16         4.08        24.23         7.00 
TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        4.50         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 
       12.10         1.78        14.07        16.80        14.96        13.87 
TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        9.40         8.88        18.97         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        18.08        16.77        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 
       14.40        15.78         2.53         1.22         0.66         4.77 
TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
       15.39         0.10        19.50         1.18         4.67        12.69 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 
       16.93        12.23        20.78        15.02        15.95         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4213 
       22.78        25.18        21.14        20.32         3.72        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 
        3.45        20.91         4.34        14.33         7.50         4.80 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 
        4.54        17.59         3.09         3.65         9.17        47.93 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        2.53        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 
       18.64        36.20         7.63         2.83        14.73         2.50 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
       20.38         6.94        22.72        33.67        12.95        25.35 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 
       26.70        11.90         0.20        10.29         2.20         2.33 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 
       10.65         5.85        11.41        19.66         3.29         4.47 
TCGA-06-0174 TCGA-06-0178 TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 
        3.22        88.14        69.90        73.84        44.58        15.42 
TCGA-06-0192 TCGA-06-0195 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
       38.96         7.40         0.53        15.02        24.16         0.72 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 
       13.64        13.32        20.42        48.69        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       46.19         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       13.61         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 
        5.95        16.64         4.37         0.43        31.50         7.79 
TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0619 
        5.39       120.56         7.36        18.02        14.73        34.92 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 
       26.66         3.65        10.62         2.24        11.24         1.35 
TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 
        5.39        28.93         0.79        50.53         3.91        31.33 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 
       14.86         5.49         1.58         7.92         2.33         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       31.27        23.44        11.01         5.16        22.68        12.76 
TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        5.42        11.38         5.42         1.61        17.72        26.30 

  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
             3.75              0.10 
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
            30.64            120.56 
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
           12.990            11.395 
[1] "3.8 - 30.6 (13.0)"  "0.1 - 120.6 (11.4)"
[1] "hr=" "1"  
D9V2, continuous
D9V3, binary
                   cls
clus                  0   1
  SLC26A3 MUTATED     1   6
  SLC26A3 WILD-TYPE 100 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A3 MUTATED      1    6
  SLC26A3 WILD-TYPE  100  173
        clus
vv       SLC26A3 MUTATED SLC26A3 WILD-TYPE
  FEMALE               1               100
  MALE                 6               173
[1] 2 2
[1] FALSE
D9V4, binary
                   cls
clus                  0   1
  SLC26A3 MUTATED     0   6
  SLC26A3 WILD-TYPE  46 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A3 MUTATED      0    6
  SLC26A3 WILD-TYPE   46  211
     clus
vv    SLC26A3 MUTATED SLC26A3 WILD-TYPE
  NO                0                46
  YES               6               211
[1] 2 2
[1] FALSE
D9V5, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  SLC26A3 MUTATED                               1                   0
  SLC26A3 WILD-TYPE                            10                   4
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  SLC26A3 MUTATED                                 6
  SLC26A3 WILD-TYPE                             259
D9V6, multiclass
                                 clus
vv                                SLC26A3 MUTATED SLC26A3 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 1                10
  TREATED PRIMARY GBM                           0                 4
  UNTREATED PRIMARY (DE NOVO) GBM               6               259
[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"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC26A3 MUTATED       0                         0     7
  SLC26A3 WILD-TYPE     5                        17   245
D9V7, multiclass
                           clus
vv                          SLC26A3 MUTATED SLC26A3 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                17
  WHITE                                   7               245
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                   cls
clus                  0   1
  SLC26A3 MUTATED     0   6
  SLC26A3 WILD-TYPE   3 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A3 MUTATED      0    6
  SLC26A3 WILD-TYPE    3  216
                        clus
vv                       SLC26A3 MUTATED SLC26A3 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               6               216
[1] 2 2
[1] FALSE

Clustering(10) Variable = SEMG1 MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2               0   1
  SEMG1 MUTATED     2   6
  SEMG1 WILD-TYPE  57 212
  SEMG1 MUTATED SEMG1 WILD-TYPE 
              8             269 
  SEMG1 MUTATED SEMG1 WILD-TYPE 
              6             212 
$`SEMG1 MUTATED`
TCGA-19-2624 TCGA-32-1979 TCGA-32-2632 TCGA-41-2575 TCGA-06-0158 TCGA-06-0185 
        0.16        19.50         8.84         9.53        10.82        73.84 
TCGA-06-0195 TCGA-06-0876 
        7.40        46.19 

$`SEMG1 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 
        1.55         4.77         4.96        15.35        22.19        15.22 
TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 
       11.97         0.95        23.05        13.78         2.89         1.38 
TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 
       58.78        40.96        17.85         7.63         7.17        17.49 
TCGA-14-3476 TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 
        0.39         3.42        29.03        25.38         5.06         9.67 
TCGA-19-2620 TCGA-19-2623 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 
        4.87         7.53         4.08        24.23         7.00         4.50 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 
        1.78        14.07        16.80        14.96        13.87         9.40 
TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        8.88        18.97         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       18.08        16.77        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 
       15.78         2.53         1.22         0.66         4.77        15.39 
TCGA-32-1977 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 
        0.10         1.18         4.67        12.69        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       20.78        15.02        15.95        22.78        25.18        21.14 
TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       20.32         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
        0.85        13.35         8.94         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        0.20        15.12        12.46         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 
       14.33         7.50         4.80         4.54        17.59         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.65         9.17        47.93         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29         2.70        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 
        5.03        23.90        34.45        18.64        36.20         7.63 
TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 
        4.73         2.83        14.73         2.50        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 
       15.45        20.32         2.70         6.15        20.38         6.94 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 
       22.72        33.67        12.95        25.35        26.70        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 
        0.20        10.29         2.20         2.33        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 
       13.94        10.45         3.19        10.65         5.85        11.41 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 TCGA-06-0184 
       19.66         3.29         4.47         3.22        88.14        69.90 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
       44.58        15.42        38.96         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 
        0.72        13.64        13.32        20.42        48.69        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       43.46         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       13.61         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
       30.64         5.95        16.64         4.37         0.43        31.50 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 
        7.79         5.39       120.56         7.36        18.02        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 
       12.99        34.92        26.66         3.65        10.62         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 
       11.24         1.35         5.39        28.93         0.79        13.78 
TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 
       50.53         3.91        31.33        14.86         5.49         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        7.92         2.33         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 
       13.64         5.16        22.68        12.76         5.42        11.38 
TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        5.42         3.75         1.61        17.72        26.30 

  SEMG1 MUTATED SEMG1 WILD-TYPE 
           0.16            0.10 
  SEMG1 MUTATED SEMG1 WILD-TYPE 
          73.84          120.56 
  SEMG1 MUTATED SEMG1 WILD-TYPE 
         10.175          11.740 
[1] "0.2 - 73.8 (10.2)"  "0.1 - 120.6 (11.7)"
[1] "hr=" "1.5"
D10V2, continuous
D10V3, binary
                 cls
clus                0   1
  SEMG1 MUTATED     2   6
  SEMG1 WILD-TYPE  99 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEMG1 MUTATED      2    6
  SEMG1 WILD-TYPE   99  173
        clus
vv       SEMG1 MUTATED SEMG1 WILD-TYPE
  FEMALE             2              99
  MALE               6             173
[1] 2 2
[1] FALSE
D10V4, binary
                 cls
clus                0   1
  SEMG1 MUTATED     1   5
  SEMG1 WILD-TYPE  45 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEMG1 MUTATED      1    5
  SEMG1 WILD-TYPE   45  212
     clus
vv    SEMG1 MUTATED SEMG1 WILD-TYPE
  NO              1              45
  YES             5             212
[1] 2 2
[1] FALSE
D10V5, continuous
                 vv
clus              GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  SEMG1 MUTATED                               0                   0
  SEMG1 WILD-TYPE                            11                   4
                 vv
clus              UNTREATED PRIMARY (DE NOVO) GBM
  SEMG1 MUTATED                                 8
  SEMG1 WILD-TYPE                             257
D10V6, multiclass
                                 clus
vv                                SEMG1 MUTATED SEMG1 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)               0              11
  TREATED PRIMARY GBM                         0               4
  UNTREATED PRIMARY (DE NOVO) GBM             8             257
[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"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SEMG1 MUTATED       0                         1     7
  SEMG1 WILD-TYPE     5                        16   245
D10V7, multiclass
                           clus
vv                          SEMG1 MUTATED SEMG1 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             1              16
  WHITE                                 7             245
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                 cls
clus                0   1
  SEMG1 MUTATED     0   8
  SEMG1 WILD-TYPE   3 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEMG1 MUTATED      0    8
  SEMG1 WILD-TYPE    3  214
                        clus
vv                       SEMG1 MUTATED SEMG1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             8             214
[1] 2 2
[1] FALSE

Clustering(11) Variable = KDR MUTATION ANALYSIS
D11V1, survival
               sevent
clus2             0   1
  KDR MUTATED     0   8
  KDR WILD-TYPE  59 210
  KDR MUTATED KDR WILD-TYPE 
            8           269 
  KDR MUTATED KDR WILD-TYPE 
            8           210 
$`KDR MUTATED`
TCGA-12-5301 TCGA-76-6282 TCGA-06-0128 TCGA-06-0142 TCGA-06-0188 TCGA-06-0241 
        2.04        17.06        22.72         2.20        44.58        48.69 
TCGA-06-0882 TCGA-81-5910 
       20.78         1.61 

$`KDR WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 
        1.55         4.77         4.96        15.35        22.19        15.22 
TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-14-0740 
       10.95        34.92        14.53        14.93         3.22        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 
        0.95        23.05        13.78         2.89         1.38        58.78 
TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 
       40.96        17.85         7.63         7.17        17.49         0.39 
TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 
        3.42        29.03        25.38         5.06         9.67         4.87 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 
        7.53         0.16         4.08        24.23         7.00         4.50 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 
        1.78        14.07        16.80        14.96        13.87         9.40 
TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        8.88        18.97         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       18.08        16.77        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 
       15.78         2.53         1.22         0.66         4.77        15.39 
TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 
        0.10        19.50         1.18         4.67        12.69        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 
       12.23        20.78        15.02        15.95         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       25.18        21.14        20.32         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 
        3.45        20.91         4.34        14.33         7.50         4.80 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 
        4.54        17.59         3.09         3.65         9.17        47.93 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6285 
        2.53        36.85        16.70         3.29         2.70         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 
       36.20         7.63         4.73         2.83        14.73         2.50 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0126 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 
       20.38         6.94        33.67        12.95        25.35        26.70 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 
       11.90         0.20        10.29         2.33        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 
       13.94        10.45         3.19        10.82        10.65         5.85 
TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 
       11.41        19.66         3.29         4.47         3.22        88.14 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0213 
       69.90        73.84        15.42        38.96         7.40         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       15.02        24.16         0.72        13.64        13.32        20.42 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.62         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0939 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       26.76        13.61         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 
       12.56        30.64         5.95        16.64         4.37         0.43 
TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 
       31.50         7.79         5.39       120.56         7.36        18.02 
TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 
       14.73        12.99        34.92        26.66         3.65        10.62 
TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 
        2.24        11.24         1.35         5.39        28.93         0.79 
TCGA-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 
       13.78        50.53         3.91        31.33        14.86         5.49 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        1.58         7.92         2.33         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       11.01        13.64         5.16        22.68        12.76         5.42 
TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5911 TCGA-87-5896 
       11.38         5.42         3.75        17.72        26.30 

  KDR MUTATED KDR WILD-TYPE 
         1.61          0.10 
  KDR MUTATED KDR WILD-TYPE 
        48.69        120.56 
  KDR MUTATED KDR WILD-TYPE 
        18.92         11.41 
[1] "1.6 - 48.7 (18.9)"  "0.1 - 120.6 (11.4)"
[1] "hr=" "1.2"
D11V2, continuous
D11V3, binary
               cls
clus              0   1
  KDR MUTATED     1   7
  KDR WILD-TYPE 100 172
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED      1    7
  KDR WILD-TYPE  100  172
        clus
vv       KDR MUTATED KDR WILD-TYPE
  FEMALE           1           100
  MALE             7           172
[1] 2 2
[1] FALSE
D11V4, binary
               cls
clus              0   1
  KDR MUTATED     2   6
  KDR WILD-TYPE  44 211
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED      2    6
  KDR WILD-TYPE   44  211
     clus
vv    KDR MUTATED KDR WILD-TYPE
  NO            2            44
  YES           6           211
[1] 2 2
[1] FALSE
D11V5, continuous
               vv
clus            GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  KDR MUTATED                               1                   0
  KDR WILD-TYPE                            10                   4
               vv
clus            UNTREATED PRIMARY (DE NOVO) GBM
  KDR MUTATED                                 7
  KDR WILD-TYPE                             258
D11V6, multiclass
                                 clus
vv                                KDR MUTATED KDR WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)             1            10
  TREATED PRIMARY GBM                       0             4
  UNTREATED PRIMARY (DE NOVO) GBM           7           258
[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"
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KDR MUTATED       0                         0     8
  KDR WILD-TYPE     5                        17   244
D11V7, multiclass
                           clus
vv                          KDR MUTATED KDR WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0            17
  WHITE                               8           244
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
               cls
clus              0   1
  KDR MUTATED     0   7
  KDR WILD-TYPE   3 215
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED      0    7
  KDR WILD-TYPE    3  215
                        clus
vv                       KDR MUTATED KDR WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           7           215
[1] 2 2
[1] FALSE

Clustering(12) Variable = RPL5 MUTATION ANALYSIS
D12V1, survival
                sevent
clus2              0   1
  RPL5 MUTATED     2   5
  RPL5 WILD-TYPE  57 213
  RPL5 MUTATED RPL5 WILD-TYPE 
             7            270 
  RPL5 MUTATED RPL5 WILD-TYPE 
             5            213 
$`RPL5 MUTATED`
TCGA-06-5413 TCGA-14-0790 TCGA-19-5947 TCGA-02-0047 TCGA-06-0154 TCGA-06-0216 
        8.81        13.78         6.64        14.73        13.94        24.16 
TCGA-26-6174 
        2.33 

$`RPL5 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.98         8.55         5.10         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 
        4.77         4.96        15.35        22.19        15.22        10.95 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 
       34.92        14.53        14.93         3.22         2.04        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 
        0.95        23.05         2.89         1.38        58.78        40.96 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 
       17.85         7.63         7.17        17.49         0.39         3.42 
TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 
       29.03        25.38         5.06         9.67         4.87         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 TCGA-19-5950 
        0.16         4.08        24.23         7.00         4.50        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
        8.02        18.90         4.73        12.10         1.78        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 
       16.80        14.96        13.87         9.40         8.88        18.97 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        14.04        11.51        24.76        18.08        16.77 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 
       16.08         7.59         2.86        14.40        15.78         2.53 
TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 
        1.22         0.66         4.77        15.39         0.10        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        1.18         4.67        12.69        16.93        12.23        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.02        15.95         8.84        22.78        25.18        21.14 
TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       20.32         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
       11.84         0.20        15.12        12.46         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 
        4.34        14.33         7.50         4.80         4.54        17.59 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 
        3.09         3.65         9.17        47.93         2.53        36.85 
TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
       16.70         3.29         2.70        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-06-0209 TCGA-02-0003 TCGA-02-0033 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 
        7.63         4.73         2.83         2.50        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 
       15.45        20.32         2.70         6.15        20.38         6.94 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 
       22.72        33.67        12.95        25.35        26.70        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 
        0.20        10.29         2.20         2.33        46.59        12.33 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 
       10.45         3.19        10.82        10.65         5.85        11.41 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 TCGA-06-0184 
       19.66         3.29         4.47         3.22        88.14        69.90 
TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0213 
       73.84        44.58        15.42        38.96         7.40         0.53 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       15.02         0.72        13.64        13.32        20.42        48.69 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.62         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       20.78        26.76        13.61         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 
       17.65        12.56        30.64         5.95        16.64         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 
        0.43        31.50         7.79         5.39       120.56         7.36 
TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 
       18.02        14.73        12.99        34.92        26.66         3.65 
TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 
       10.62         2.24        11.24         1.35         5.39        28.93 
TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 TCGA-26-5133 
        0.79        13.78        50.53         3.91        31.33        14.86 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        5.49         1.58         7.92         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       11.01        13.64         5.16        22.68        12.76         5.42 
TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
       11.38         5.42         3.75         1.61        17.72        26.30 

  RPL5 MUTATED RPL5 WILD-TYPE 
          2.33           0.10 
  RPL5 MUTATED RPL5 WILD-TYPE 
         24.16         120.56 
  RPL5 MUTATED RPL5 WILD-TYPE 
         13.78          11.46 
[1] "2.3 - 24.2 (13.8)"  "0.1 - 120.6 (11.5)"
[1] "hr=" "1.1"
D12V2, continuous
D12V3, binary
                cls
clus               0   1
  RPL5 MUTATED     4   3
  RPL5 WILD-TYPE  97 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL5 MUTATED      4    3
  RPL5 WILD-TYPE   97  176
        clus
vv       RPL5 MUTATED RPL5 WILD-TYPE
  FEMALE            4             97
  MALE              3            176
[1] 2 2
[1] FALSE
D12V4, binary
                cls
clus               0   1
  RPL5 MUTATED     0   7
  RPL5 WILD-TYPE  46 210
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL5 MUTATED      0    7
  RPL5 WILD-TYPE   46  210
     clus
vv    RPL5 MUTATED RPL5 WILD-TYPE
  NO             0             46
  YES            7            210
[1] 2 2
[1] FALSE
D12V5, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  RPL5 MUTATED                               0                   0
  RPL5 WILD-TYPE                            11                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  RPL5 MUTATED                                 7
  RPL5 WILD-TYPE                             258
D12V6, multiclass
                                 clus
vv                                RPL5 MUTATED RPL5 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              0             11
  TREATED PRIMARY GBM                        0              4
  UNTREATED PRIMARY (DE NOVO) GBM            7            258
[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"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RPL5 MUTATED       0                         1     6
  RPL5 WILD-TYPE     5                        16   246
D12V7, multiclass
                           clus
vv                          RPL5 MUTATED RPL5 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            1             16
  WHITE                                6            246
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                cls
clus               0   1
  RPL5 MUTATED     0   6
  RPL5 WILD-TYPE   3 216
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL5 MUTATED      0    6
  RPL5 WILD-TYPE    3  216
                        clus
vv                       RPL5 MUTATED RPL5 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            6            216
[1] 2 2
[1] FALSE

Clustering(13) Variable = ATRX MUTATION ANALYSIS
D13V1, survival
                sevent
clus2              0   1
  ATRX MUTATED     9   7
  ATRX WILD-TYPE  50 211
  ATRX MUTATED ATRX WILD-TYPE 
            16            261 
  ATRX MUTATED ATRX WILD-TYPE 
             7            211 
$`ATRX MUTATED`
TCGA-06-6391 TCGA-06-5417 TCGA-06-5858 TCGA-06-6388 TCGA-06-6701 TCGA-14-1456 
        1.48         5.10         6.15         5.23         4.96        40.96 
TCGA-14-4157 TCGA-19-2629 TCGA-27-2521 TCGA-32-4208 TCGA-74-6575 TCGA-02-2483 
        3.42        24.23        16.77        21.14        20.91        15.32 
TCGA-06-0129 TCGA-06-0213 TCGA-06-2570 TCGA-15-1444 
       33.67         0.53        31.50        50.53 

$`ATRX WILD-TYPE`
TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
       15.32        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5859 TCGA-06-6695 
        8.98         8.55         2.73         3.75         4.57         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-12-0615 TCGA-12-1597 
       12.85         4.77         1.55         4.77        15.35        22.19 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       15.22        10.95        34.92        14.53        14.93         3.22 
TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 
        2.04        11.97         0.95        23.05        13.78         2.89 
TCGA-14-1395 TCGA-14-1450 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 
        1.38        58.78        17.85         7.63         7.17        17.49 
TCGA-14-3476 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 
        0.39        29.03        25.38         5.06         9.67         4.87 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 
        7.53         0.16         4.08         7.00         4.50         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 
       14.07        16.80        14.96        13.87         9.40         8.88 
TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       18.97         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 
       16.08         7.59         2.86        14.40        15.78         2.53 
TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 
        1.22         0.66         4.77        15.39         0.10        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        1.18         4.67        12.69        16.93        12.23        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4209 
       15.02        15.95         8.84        22.78        25.18        20.32 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6577 TCGA-74-6578 
        0.20        15.12        12.46         3.45         4.34        14.33 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 
        7.50         4.80         4.54        17.59         3.09         3.65 
TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        9.17        47.93         2.53        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
        2.70        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 
       23.90        34.45        18.64        36.20         7.63         4.73 
TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 
        2.83        14.73         2.50        12.92        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 TCGA-06-0130 
        2.70         6.15        20.38         6.94        22.72        12.95 
TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       25.35        26.70        11.90         0.20        10.29         2.20 
TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
        2.33        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 
       10.82        10.65         5.85        11.41        19.66         3.29 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 
        4.47         3.22        88.14        69.90        73.84        44.58 
TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
       15.42        38.96         7.40        15.02        24.16         0.72 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 
       13.64        13.32        20.42        48.69        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       46.19         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       13.61         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-6389 
       30.64         5.95        16.64         4.37         0.43         7.79 
TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 
        5.39       120.56         7.36        18.02        14.73        12.99 
TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 
       34.92        26.66         3.65        10.62         2.24        11.24 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 TCGA-16-0846 
        1.35         5.39        28.93         0.79        13.78         3.91 
TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
       31.33        14.86         5.49         1.58         7.92         2.33 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        23.44        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 
       22.68        12.76         5.42        11.38         5.42         3.75 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

  ATRX MUTATED ATRX WILD-TYPE 
          0.53           0.10 
  ATRX MUTATED ATRX WILD-TYPE 
         50.53         120.56 
  ATRX MUTATED ATRX WILD-TYPE 
        16.045         11.410 
[1] "0.5 - 50.5 (16.0)"  "0.1 - 120.6 (11.4)"
[1] "hr=" "2.5"
D13V2, continuous
D13V3, binary
                cls
clus               0   1
  ATRX MUTATED     7   9
  ATRX WILD-TYPE  94 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED      7    9
  ATRX WILD-TYPE   94  170
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  FEMALE            7             94
  MALE              9            170
[1] 2 2
[1] FALSE
D13V4, binary
                cls
clus               0   1
  ATRX MUTATED     2  14
  ATRX WILD-TYPE  44 203
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED      2   14
  ATRX WILD-TYPE   44  203
     clus
vv    ATRX MUTATED ATRX WILD-TYPE
  NO             2             44
  YES           14            203
[1] 2 2
[1] FALSE
D13V5, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  ATRX MUTATED                               1                   0
  ATRX WILD-TYPE                            10                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  ATRX MUTATED                                15
  ATRX WILD-TYPE                             250
D13V6, multiclass
                                 clus
vv                                ATRX MUTATED ATRX WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              1             10
  TREATED PRIMARY GBM                        0              4
  UNTREATED PRIMARY (DE NOVO) GBM           15            250
[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"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATRX MUTATED       2                         1    12
  ATRX WILD-TYPE     3                        16   240
D13V7, multiclass
                           clus
vv                          ATRX MUTATED ATRX WILD-TYPE
  ASIAN                                2              3
  BLACK OR AFRICAN AMERICAN            1             16
  WHITE                               12            240
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                cls
clus               0   1
  ATRX MUTATED     0  13
  ATRX WILD-TYPE   3 209
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED      0   13
  ATRX WILD-TYPE    3  209
                        clus
vv                       ATRX MUTATED ATRX WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           13            209
[1] 2 2
[1] FALSE

Clustering(14) Variable = MAP3K1 MUTATION ANALYSIS
D14V1, survival
                  sevent
clus2                0   1
  MAP3K1 MUTATED     1   5
  MAP3K1 WILD-TYPE  58 213
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
               6              271 
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
               5              213 
$`MAP3K1 MUTATED`
TCGA-14-0790 TCGA-06-0214 TCGA-06-0743 TCGA-06-2559 TCGA-12-0619 TCGA-26-6173 
       13.78        15.02        26.40         4.93        34.92         7.92 

$`MAP3K1 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 
        1.55         4.77         4.96        15.35        22.19        15.22 
TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 
       11.97         0.95        23.05         2.89         1.38        58.78 
TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 
       40.96        17.85         7.63         7.17        17.49         0.39 
TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 
        3.42        29.03        25.38         5.06         9.67         4.87 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 
        7.53         0.16         4.08        24.23         7.00         4.50 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 
        1.78        14.07        16.80        14.96        13.87         9.40 
TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        8.88        18.97         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       18.08        16.77        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 
       15.78         2.53         1.22         0.66         4.77        15.39 
TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 
        0.10        19.50         1.18         4.67        12.69        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 
       12.23        20.78        15.02        15.95         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       25.18        21.14        20.32         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 
        3.45        20.91         4.34        14.33         7.50         4.80 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 
        4.54        17.59         3.09         3.65         9.17        47.93 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        2.53        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 
       18.64        36.20         7.63         4.73         2.83        14.73 
TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
        2.50        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
        6.15        20.38         6.94        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       25.35        26.70        11.90         0.20        10.29         2.20 
TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
        2.33        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 
       10.82        10.65         5.85        11.41        19.66         3.29 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 
        4.47         3.22        88.14        69.90        73.84        44.58 
TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0213 TCGA-06-0216 TCGA-06-0219 
       15.42        38.96         7.40         0.53        24.16         0.72 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 
       13.64        13.32        20.42        48.69        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0744 
        5.75         9.80         2.10        23.57        14.20        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 
        7.17        40.41        16.57        20.78        26.76        13.61 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
        1.08        12.49        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 
       16.64         4.37         0.43        31.50         7.79         5.39 
TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0688 
      120.56         7.36        18.02        14.73        12.99        26.66 
TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 
        3.65        10.62         2.24        11.24         1.35         5.39 
TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 
       28.93         0.79        13.78        50.53         3.91        31.33 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 
       14.86         5.49         1.58         2.33         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        12.76 
TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 
        5.42        11.38         5.42         3.75         1.61        17.72 
TCGA-87-5896 
       26.30 

  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
            4.93             0.10 
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
           34.92           120.56 
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
           14.40            11.41 
[1] "4.9 - 34.9 (14.4)"  "0.1 - 120.6 (11.4)"
[1] "hr=" "1.2"
D14V2, continuous
D14V3, binary
                  cls
clus                 0   1
  MAP3K1 MUTATED     1   5
  MAP3K1 WILD-TYPE 100 174
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K1 MUTATED      1    5
  MAP3K1 WILD-TYPE  100  174
        clus
vv       MAP3K1 MUTATED MAP3K1 WILD-TYPE
  FEMALE              1              100
  MALE                5              174
[1] 2 2
[1] FALSE
D14V4, binary
                  cls
clus                 0   1
  MAP3K1 MUTATED     1   5
  MAP3K1 WILD-TYPE  45 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K1 MUTATED      1    5
  MAP3K1 WILD-TYPE   45  212
     clus
vv    MAP3K1 MUTATED MAP3K1 WILD-TYPE
  NO               1               45
  YES              5              212
[1] 2 2
[1] FALSE
D14V5, continuous
                  vv
clus               GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  MAP3K1 MUTATED                               0                   0
  MAP3K1 WILD-TYPE                            11                   4
                  vv
clus               UNTREATED PRIMARY (DE NOVO) GBM
  MAP3K1 MUTATED                                 6
  MAP3K1 WILD-TYPE                             259
D14V6, multiclass
                                 clus
vv                                MAP3K1 MUTATED MAP3K1 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                0               11
  TREATED PRIMARY GBM                          0                4
  UNTREATED PRIMARY (DE NOVO) GBM              6              259
[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"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAP3K1 MUTATED       0                         0     6
  MAP3K1 WILD-TYPE     5                        17   246
D14V7, multiclass
                           clus
vv                          MAP3K1 MUTATED MAP3K1 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0               17
  WHITE                                  6              246
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                  cls
clus                 0   1
  MAP3K1 MUTATED     0   5
  MAP3K1 WILD-TYPE   3 217
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K1 MUTATED      0    5
  MAP3K1 WILD-TYPE    3  217
                        clus
vv                       MAP3K1 MUTATED MAP3K1 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              5              217
[1] 2 2
[1] FALSE

Clustering(15) Variable = BRAF MUTATION ANALYSIS
D15V1, survival
                sevent
clus2              0   1
  BRAF MUTATED     1   5
  BRAF WILD-TYPE  58 213
  BRAF MUTATED BRAF WILD-TYPE 
             6            271 
  BRAF MUTATED BRAF WILD-TYPE 
             5            213 
$`BRAF MUTATED`
TCGA-06-1806 TCGA-76-4928 TCGA-02-0047 TCGA-06-0151 TCGA-06-0185 TCGA-06-0644 
       15.32         3.09        14.73        46.59        73.84        12.62 

$`BRAF WILD-TYPE`
TCGA-06-6391 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 TCGA-06-5413 
        1.48        11.74         3.55         8.35         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.98         8.55         5.10         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 
        4.77         4.96        15.35        22.19        15.22        10.95 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 
       34.92        14.53        14.93         3.22         2.04        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 
        0.95        23.05        13.78         2.89         1.38        58.78 
TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 
       40.96        17.85         7.63         7.17        17.49         0.39 
TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 
        3.42        29.03        25.38         5.06         9.67         4.87 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 
        7.53         0.16         4.08        24.23         7.00         4.50 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 
        1.78        14.07        16.80        14.96        13.87         9.40 
TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        8.88        18.97         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       18.08        16.77        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 
       15.78         2.53         1.22         0.66         4.77        15.39 
TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 
        0.10        19.50         1.18         4.67        12.69        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 
       12.23        20.78        15.02        15.95         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       25.18        21.14        20.32         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 
        3.45        20.91         4.34        14.33         7.50         4.80 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 
        4.54        17.59         3.65         9.17        47.93         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 
       36.85        16.70         3.29         2.70        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 TCGA-02-0033 TCGA-02-0055 TCGA-02-2470 
       36.20         7.63         4.73         2.83         2.50        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 
        6.94        22.72        33.67        12.95        25.35        26.70 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0152 
       11.90         0.20        10.29         2.20         2.33        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 
       13.94        10.45         3.19        10.82        10.65         5.85 
TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 
       11.41        19.66         3.29         4.47         3.22        88.14 
TCGA-06-0184 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0213 
       69.90        44.58        15.42        38.96         7.40         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       15.02        24.16         0.72        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       48.69         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       20.78        26.76        13.61         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 
       17.65        12.56        30.64         5.95        16.64         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 
        0.43        31.50         7.79         5.39       120.56         7.36 
TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 
       18.02        14.73        12.99        34.92        26.66         3.65 
TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 
       10.62         2.24        11.24         1.35         5.39        28.93 
TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 TCGA-26-5133 
        0.79        13.78        50.53         3.91        31.33        14.86 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 
        5.49         1.58         7.92         2.33         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        12.76 
TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 
        5.42        11.38         5.42         3.75         1.61        17.72 
TCGA-87-5896 
       26.30 

  BRAF MUTATED BRAF WILD-TYPE 
          3.09           0.10 
  BRAF MUTATED BRAF WILD-TYPE 
         73.84         120.56 
  BRAF MUTATED BRAF WILD-TYPE 
        15.025         11.380 
[1] "3.1 - 73.8 (15.0)"  "0.1 - 120.6 (11.4)"
[1] "hr=" "1.7"
D15V2, continuous
D15V3, binary
                cls
clus               0   1
  BRAF MUTATED     2   4
  BRAF WILD-TYPE  99 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      2    4
  BRAF WILD-TYPE   99  175
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE            2             99
  MALE              4            175
[1] 2 2
[1] FALSE
D15V4, binary
                cls
clus               0   1
  BRAF MUTATED     0   6
  BRAF WILD-TYPE  46 211
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      0    6
  BRAF WILD-TYPE   46  211
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO             0             46
  YES            6            211
[1] 2 2
[1] FALSE
D15V5, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  BRAF MUTATED                               2                   0
  BRAF WILD-TYPE                             9                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  BRAF MUTATED                                 4
  BRAF WILD-TYPE                             261
D15V6, multiclass
                                 clus
vv                                BRAF MUTATED BRAF WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              2              9
  TREATED PRIMARY GBM                        0              4
  UNTREATED PRIMARY (DE NOVO) GBM            4            261
[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"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED       0                         1     5
  BRAF WILD-TYPE     5                        16   247
D15V7, multiclass
                           clus
vv                          BRAF MUTATED BRAF WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            1             16
  WHITE                                5            247
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                cls
clus               0   1
  BRAF MUTATED     0   5
  BRAF WILD-TYPE   3 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      0    5
  BRAF WILD-TYPE    3  217
                        clus
vv                       BRAF MUTATED BRAF WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            5            217
[1] 2 2
[1] FALSE

Clustering(16) Variable = EGFR MUTATION ANALYSIS
D16V1, survival
                sevent
clus2              0   1
  EGFR MUTATED    14  59
  EGFR WILD-TYPE  45 159
  EGFR MUTATED EGFR WILD-TYPE 
            73            204 
  EGFR MUTATED EGFR WILD-TYPE 
            59            159 
$`EGFR MUTATED`
TCGA-06-5413 TCGA-06-5856 TCGA-06-6695 TCGA-06-6700 TCGA-12-3650 TCGA-12-3652 
        8.81         3.75         8.32         4.77        10.95        34.92 
TCGA-14-0786 TCGA-14-0790 TCGA-14-1395 TCGA-14-1456 TCGA-14-1823 TCGA-14-1829 
       23.05        13.78         1.38        40.96        17.85         7.17 
TCGA-14-2554 TCGA-16-1045 TCGA-19-1790 TCGA-19-2620 TCGA-19-2624 TCGA-19-2625 
       17.49        29.03         5.06         4.87         0.16         4.08 
TCGA-26-1439 TCGA-27-1831 TCGA-27-1838 TCGA-27-2528 TCGA-28-1747 TCGA-32-1970 
       13.87        16.60        11.51        15.78         2.53        15.39 
TCGA-32-1979 TCGA-32-1982 TCGA-32-1991 TCGA-32-2632 TCGA-76-4926 TCGA-76-4927 
       19.50         4.67        16.93         8.84         4.54        17.59 
TCGA-76-4931 TCGA-76-6191 TCGA-76-6282 TCGA-76-6656 TCGA-76-6661 TCGA-02-0003 
        9.17        16.70        17.06         4.83        23.90         4.73 
TCGA-02-2485 TCGA-06-0137 TCGA-06-0142 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
       15.45        26.70         2.20        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0174 TCGA-06-0185 TCGA-06-0237 TCGA-06-0649 TCGA-06-0650 
       10.82         3.22        73.84        13.64         2.10        23.57 
TCGA-06-0743 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0876 TCGA-06-0878 
       26.40         2.70         2.70         0.92        46.19         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-1804 TCGA-06-2557 TCGA-06-2561 TCGA-06-2563 
       40.41        16.57        13.61         1.08        17.65        30.64 
TCGA-06-2565 TCGA-06-2567 TCGA-12-0616 TCGA-12-0619 TCGA-14-0789 TCGA-14-0813 
       16.64         4.37        14.73        34.92        11.24         1.35 
TCGA-15-0742 TCGA-26-5139 TCGA-28-5207 TCGA-28-5209 TCGA-28-5213 TCGA-81-5910 
       13.78         1.58        11.28        14.53        31.27         1.61 
TCGA-81-5911 
       17.72 

$`EGFR WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 
        8.98         8.55         5.10         2.73         6.15         4.57 
TCGA-06-6388 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6701 TCGA-12-0615 
        5.23        12.85         4.77         1.55         4.96        15.35 
TCGA-12-1597 TCGA-12-3649 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       22.19        15.22        14.53        14.93         3.22         2.04 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0862 TCGA-14-1450 TCGA-14-1825 TCGA-14-3476 
       11.97         0.95         2.89        58.78         7.63         0.39 
TCGA-14-4157 TCGA-19-1390 TCGA-19-2619 TCGA-19-2623 TCGA-19-2629 TCGA-19-2631 
        3.42        25.38         9.67         7.53        24.23         7.00 
TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        4.50         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-5132 
       12.10         1.78        14.07        16.80        14.96         9.40 
TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
        8.88        18.97         5.06         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       21.30        30.05        14.04        24.76        18.08        16.77 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-28-1753 TCGA-28-2502 
       16.08         7.59         2.86        14.40         1.22         0.66 
TCGA-28-2509 TCGA-32-1977 TCGA-32-1980 TCGA-32-1986 TCGA-32-2491 TCGA-32-2494 
        4.77         0.10         1.18        12.69        12.23        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 
       15.02        15.95        22.78        25.18        21.14        20.32 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        0.20        15.12        12.46         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 TCGA-76-4928 TCGA-76-4929 TCGA-76-4932 
       14.33         7.50         4.80         3.09         3.65        47.93 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6192 TCGA-76-6193 TCGA-76-6285 TCGA-76-6286 
        2.53        36.85         3.29         2.70         8.35        20.98 
TCGA-76-6657 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 TCGA-02-0033 
        5.03        34.45        18.64        36.20         7.63         2.83 
TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 TCGA-02-2486 TCGA-06-0119 
       14.73         2.50        12.92        15.32        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
        6.15        20.38         6.94        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0145 TCGA-06-0151 
       25.35        11.90         0.20        10.29         2.33        46.59 
TCGA-06-0152 TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 
       12.33        10.65         5.85        11.41        19.66         3.29 
TCGA-06-0173 TCGA-06-0178 TCGA-06-0184 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 
        4.47        88.14        69.90        44.58        15.42        38.96 
TCGA-06-0195 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0238 
        7.40         0.53        15.02        24.16         0.72        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
       20.42        48.69        12.62         5.75         5.75         9.80 
TCGA-06-0686 TCGA-06-0744 TCGA-06-0745 TCGA-06-0875 TCGA-06-0882 TCGA-06-0939 
       14.20        46.88         7.86        43.46        20.78        26.76 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2562 TCGA-06-2564 TCGA-06-2569 TCGA-06-2570 
       12.49         4.93        12.56         5.95         0.43        31.50 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0618 
        7.79         5.39       120.56         7.36        18.02        12.99 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0817 TCGA-14-0871 
       26.66         3.65        10.62         2.24         5.39        28.93 
TCGA-14-1043 TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 
        0.79        50.53         3.91        31.33        14.86         5.49 
TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5208 
        7.92         2.33         7.30         5.26        14.93        17.88 
TCGA-28-5211 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       11.77        23.44        11.01        13.64         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-87-5896 
       12.76         5.42        11.38         5.42         3.75        26.30 

  EGFR MUTATED EGFR WILD-TYPE 
          0.16           0.10 
  EGFR MUTATED EGFR WILD-TYPE 
         73.84         120.56 
  EGFR MUTATED EGFR WILD-TYPE 
        13.610         11.395 
[1] "0.2 - 73.8 (13.6)"  "0.1 - 120.6 (11.4)"
[1] "hr=" "1"  
D16V2, continuous
D16V3, binary
                cls
clus               0   1
  EGFR MUTATED    22  51
  EGFR WILD-TYPE  79 128
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     22   51
  EGFR WILD-TYPE   79  128
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  FEMALE           22             79
  MALE             51            128
[1] 2 2
[1] FALSE
D16V4, binary
                cls
clus               0   1
  EGFR MUTATED    12  57
  EGFR WILD-TYPE  34 160
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     12   57
  EGFR WILD-TYPE   34  160
     clus
vv    EGFR MUTATED EGFR WILD-TYPE
  NO            12             34
  YES           57            160
[1] 2 2
[1] FALSE
D16V5, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  EGFR MUTATED                               1                   0
  EGFR WILD-TYPE                            10                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  EGFR MUTATED                                72
  EGFR WILD-TYPE                             193
D16V6, multiclass
                                 clus
vv                                EGFR MUTATED EGFR WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              1             10
  TREATED PRIMARY GBM                        0              4
  UNTREATED PRIMARY (DE NOVO) GBM           72            193
[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"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EGFR MUTATED       1                         7    65
  EGFR WILD-TYPE     4                        10   187
D16V7, multiclass
                           clus
vv                          EGFR MUTATED EGFR WILD-TYPE
  ASIAN                                1              4
  BLACK OR AFRICAN AMERICAN            7             10
  WHITE                               65            187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                cls
clus               0   1
  EGFR MUTATED     0  53
  EGFR WILD-TYPE   3 169
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      0   53
  EGFR WILD-TYPE    3  169
                        clus
vv                       EGFR MUTATED EGFR WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           53            169
[1] 2 2
[1] FALSE

Clustering(17) Variable = TMPRSS6 MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  TMPRSS6 MUTATED     3   3
  TMPRSS6 WILD-TYPE  56 215
  TMPRSS6 MUTATED TMPRSS6 WILD-TYPE 
                6               271 
  TMPRSS6 MUTATED TMPRSS6 WILD-TYPE 
                3               215 
$`TMPRSS6 MUTATED`
TCGA-06-5415 TCGA-19-2629 TCGA-27-1832 TCGA-76-4928 TCGA-06-0878 TCGA-26-5139 
        8.55        24.23         9.86         3.09         7.17         1.58 

$`TMPRSS6 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.81         8.98         5.10         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 
        4.77         4.96        15.35        22.19        15.22        10.95 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 
       34.92        14.53        14.93         3.22         2.04        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 
        0.95        23.05        13.78         2.89         1.38        58.78 
TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 
       40.96        17.85         7.63         7.17        17.49         0.39 
TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 
        3.42        29.03        25.38         5.06         9.67         4.87 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 
        7.53         0.16         4.08         7.00         4.50         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 
       14.07        16.80        14.96        13.87         9.40         8.88 
TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
       18.97         5.06        16.60        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        14.04        11.51        24.76        18.08        16.77 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 
       16.08         7.59         2.86        14.40        15.78         2.53 
TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 
        1.22         0.66         4.77        15.39         0.10        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        1.18         4.67        12.69        16.93        12.23        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.02        15.95         8.84        22.78        25.18        21.14 
TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       20.32         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
       11.84         0.20        15.12        12.46         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 
        4.34        14.33         7.50         4.80         4.54        17.59 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.65         9.17        47.93         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29         2.70        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 
        5.03        23.90        34.45        18.64        36.20         7.63 
TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 
        4.73         2.83        14.73         2.50        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 
       15.45        20.32         2.70         6.15        20.38         6.94 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 
       22.72        33.67        12.95        25.35        26.70        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 
        0.20        10.29         2.20         2.33        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 
       13.94        10.45         3.19        10.82        10.65         5.85 
TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 
       11.41        19.66         3.29         4.47         3.22        88.14 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 
       69.90        73.84        44.58        15.42        38.96         7.40 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 
        0.53        15.02        24.16         0.72        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
       20.42        48.69        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.10        23.57        14.20        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0879 
        2.70         2.70         0.92        43.46        46.19        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 
       16.57        20.78        26.76        13.61         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 
        4.37         0.43        31.50         7.79         5.39       120.56 
TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 
        7.36        18.02        14.73        12.99        34.92        26.66 
TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 
        3.65        10.62         2.24        11.24         1.35         5.39 
TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 
       28.93         0.79        13.78        50.53         3.91        31.33 
TCGA-26-5133 TCGA-26-5134 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 
       14.86         5.49         7.92         2.33         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        12.76 
TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 
        5.42        11.38         5.42         3.75         1.61        17.72 
TCGA-87-5896 
       26.30 

  TMPRSS6 MUTATED TMPRSS6 WILD-TYPE 
             1.58              0.10 
  TMPRSS6 MUTATED TMPRSS6 WILD-TYPE 
            24.23            120.56 
  TMPRSS6 MUTATED TMPRSS6 WILD-TYPE 
             7.86             11.77 
[1] "1.6 - 24.2 (7.9)"   "0.1 - 120.6 (11.8)"
[1] "hr=" "1"  
D17V2, continuous
D17V3, binary
                   cls
clus                  0   1
  TMPRSS6 MUTATED     3   3
  TMPRSS6 WILD-TYPE  98 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS6 MUTATED      3    3
  TMPRSS6 WILD-TYPE   98  176
        clus
vv       TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  FEMALE               3                98
  MALE                 3               176
[1] 2 2
[1] FALSE
D17V4, binary
                   cls
clus                  0   1
  TMPRSS6 MUTATED     1   5
  TMPRSS6 WILD-TYPE  45 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS6 MUTATED      1    5
  TMPRSS6 WILD-TYPE   45  212
     clus
vv    TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  NO                1                45
  YES               5               212
[1] 2 2
[1] FALSE
D17V5, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  TMPRSS6 MUTATED                               0                   0
  TMPRSS6 WILD-TYPE                            11                   4
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  TMPRSS6 MUTATED                                 6
  TMPRSS6 WILD-TYPE                             259
D17V6, multiclass
                                 clus
vv                                TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                11
  TREATED PRIMARY GBM                           0                 4
  UNTREATED PRIMARY (DE NOVO) GBM               6               259
[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"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMPRSS6 MUTATED       0                         0     6
  TMPRSS6 WILD-TYPE     5                        17   246
D17V7, multiclass
                           clus
vv                          TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                17
  WHITE                                   6               246
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                   cls
clus                  0   1
  TMPRSS6 MUTATED     0   5
  TMPRSS6 WILD-TYPE   3 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS6 MUTATED      0    5
  TMPRSS6 WILD-TYPE    3  217
                        clus
vv                       TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               5               217
[1] 2 2
[1] FALSE

Clustering(18) Variable = PRKCD MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2               0   1
  PRKCD MUTATED     2   1
  PRKCD WILD-TYPE  57 217
  PRKCD MUTATED PRKCD WILD-TYPE 
              3             274 
  PRKCD MUTATED PRKCD WILD-TYPE 
              1             217 
$`PRKCD MUTATED`
TCGA-14-4157 TCGA-06-0145 TCGA-26-5133 
        3.42         2.33        14.86 

$`PRKCD WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 
        1.55         4.77         4.96        15.35        22.19        15.22 
TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 
       11.97         0.95        23.05        13.78         2.89         1.38 
TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 
       58.78        40.96        17.85         7.63         7.17        17.49 
TCGA-14-3476 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 
        0.39        29.03        25.38         5.06         9.67         4.87 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 
        7.53         0.16         4.08        24.23         7.00         4.50 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 
        1.78        14.07        16.80        14.96        13.87         9.40 
TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        8.88        18.97         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       18.08        16.77        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 
       15.78         2.53         1.22         0.66         4.77        15.39 
TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 
        0.10        19.50         1.18         4.67        12.69        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 
       12.23        20.78        15.02        15.95         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       25.18        21.14        20.32         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 
        3.45        20.91         4.34        14.33         7.50         4.80 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 
        4.54        17.59         3.09         3.65         9.17        47.93 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        2.53        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 
       18.64        36.20         7.63         4.73         2.83        14.73 
TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
        2.50        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
        6.15        20.38         6.94        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       25.35        26.70        11.90         0.20        10.29         2.20 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 
       10.65         5.85        11.41        19.66         3.29         4.47 
TCGA-06-0174 TCGA-06-0178 TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 
        3.22        88.14        69.90        73.84        44.58        15.42 
TCGA-06-0192 TCGA-06-0195 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
       38.96         7.40         0.53        15.02        24.16         0.72 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 
       13.64        13.32        20.42        48.69        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       46.19         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       13.61         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
       30.64         5.95        16.64         4.37         0.43        31.50 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 
        7.79         5.39       120.56         7.36        18.02        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 
       12.99        34.92        26.66         3.65        10.62         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 
       11.24         1.35         5.39        28.93         0.79        13.78 
TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 
       50.53         3.91        31.33         5.49         1.58         7.92 
TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        2.33         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 
        5.16        22.68        12.76         5.42        11.38         5.42 
TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        3.75         1.61        17.72        26.30 

  PRKCD MUTATED PRKCD WILD-TYPE 
           2.33            0.10 
  PRKCD MUTATED PRKCD WILD-TYPE 
          14.86          120.56 
  PRKCD MUTATED PRKCD WILD-TYPE 
          3.420          11.625 
[1] "2.3 - 14.9 (3.4)"   "0.1 - 120.6 (11.6)"
[1] "hr=" "1"  
D18V2, continuous
D18V3, binary
                 cls
clus                0   1
  PRKCD MUTATED     1   2
  PRKCD WILD-TYPE 100 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      1    2
  PRKCD WILD-TYPE  100  177
        clus
vv       PRKCD MUTATED PRKCD WILD-TYPE
  FEMALE             1             100
  MALE               2             177
[1] 2 2
[1] FALSE
D18V4, binary
                 cls
clus                0   1
  PRKCD MUTATED     1   2
  PRKCD WILD-TYPE  45 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      1    2
  PRKCD WILD-TYPE   45  215
     clus
vv    PRKCD MUTATED PRKCD WILD-TYPE
  NO              1              45
  YES             2             215
[1] 2 2
[1] FALSE
D18V5, continuous
[1] "Remove cluster labels:" "PRKCD MUTATED"         
clus
  PRKCD MUTATED PRKCD WILD-TYPE 
              2             204 
     TCGA-06-1806      TCGA-06-5408      TCGA-06-5410      TCGA-06-5411 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5412      TCGA-06-5413      TCGA-06-5414      TCGA-06-5415 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5417      TCGA-06-5418      TCGA-06-5858      TCGA-06-5859 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-6388      TCGA-06-6695      TCGA-06-6697      TCGA-06-6700 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-12-0615      TCGA-12-1597      TCGA-12-3649      TCGA-12-3650 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-12-3652      TCGA-12-3653      TCGA-12-5299      TCGA-12-5301 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-14-0740      TCGA-14-0786      TCGA-14-0790      TCGA-14-0862 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-14-1395      TCGA-14-1450      TCGA-14-1456      TCGA-14-1823 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-14-1825      TCGA-14-1829      TCGA-14-2554      TCGA-19-1390 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-1790      TCGA-19-2619      TCGA-19-2620      TCGA-19-2623 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-2631      TCGA-19-4068      TCGA-19-5947      TCGA-19-5950 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-5951      TCGA-19-5952      TCGA-19-5954      TCGA-19-5958 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-5959      TCGA-19-5960      TCGA-26-5132      TCGA-27-1830 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-27-1831      TCGA-27-1832      TCGA-27-1833      TCGA-27-1834 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-27-1835      TCGA-27-1836      TCGA-27-1837      TCGA-27-1838 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-27-2518      TCGA-27-2519      TCGA-27-2521      TCGA-27-2523 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-27-2524      TCGA-27-2526      TCGA-27-2527      TCGA-27-2528 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-28-2502      TCGA-28-2509      TCGA-32-1982      TCGA-32-1986 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-32-2615      TCGA-32-2638      TCGA-32-4213      TCGA-41-2571 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-41-2573      TCGA-41-2575      TCGA-74-6573      TCGA-74-6575 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-74-6577      TCGA-74-6578      TCGA-74-6584      TCGA-76-4925 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-4926      TCGA-76-4927      TCGA-76-4928      TCGA-76-4929 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-4931      TCGA-76-4932      TCGA-76-4934      TCGA-76-4935 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-6191      TCGA-76-6192      TCGA-76-6193      TCGA-76-6282 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-6285      TCGA-76-6286      TCGA-76-6656      TCGA-76-6657 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-6661      TCGA-76-6662      TCGA-76-6663      TCGA-76-6664 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-02-0003      TCGA-02-0033      TCGA-02-0047      TCGA-02-0055 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-02-2470      TCGA-02-2483      TCGA-02-2485      TCGA-02-2486 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0126      TCGA-06-0128      TCGA-06-0129      TCGA-06-0130 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0139      TCGA-06-0140      TCGA-06-0141      TCGA-06-0151 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0154      TCGA-06-0155      TCGA-06-0157      TCGA-06-0158 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0165      TCGA-06-0167      TCGA-06-0168      TCGA-06-0169 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0174      TCGA-06-0178      TCGA-06-0184      TCGA-06-0185 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0188      TCGA-06-0192      TCGA-06-0195      TCGA-06-0214 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0216      TCGA-06-0238      TCGA-06-0240      TCGA-06-0241 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0644      TCGA-06-0646      TCGA-06-0648      TCGA-06-0686 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0743      TCGA-06-0744      TCGA-06-0745      TCGA-06-0747 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0750      TCGA-06-0875      TCGA-06-0876      TCGA-06-0878 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0879      TCGA-06-0881      TCGA-06-0882      TCGA-06-0939 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-2557      TCGA-06-2558      TCGA-06-2559      TCGA-06-2561 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-2562      TCGA-06-2563      TCGA-06-2564      TCGA-06-2565 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-2567      TCGA-06-2569      TCGA-06-2570      TCGA-06-6389 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-6390      TCGA-08-0386      TCGA-12-0616      TCGA-12-0618 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-12-0619      TCGA-12-0688      TCGA-12-0692      TCGA-12-0821 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-14-0787      TCGA-14-0789      TCGA-14-0813      TCGA-14-0817 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-14-0871      TCGA-14-1043      TCGA-15-0742      TCGA-26-1442 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-26-5134      TCGA-26-5139      TCGA-26-6173      TCGA-26-6174 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-28-2513      TCGA-28-2514      TCGA-28-5204      TCGA-28-5207 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-28-5208      TCGA-28-5211      TCGA-28-5213      TCGA-28-5214 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-28-5215      TCGA-28-5216      TCGA-28-5219      TCGA-28-5220 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-6280      TCGA-76-6283      TCGA-76-6660      TCGA-81-5910 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
                 vv
clus              GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  PRKCD MUTATED                               0                   0
  PRKCD WILD-TYPE                            11                   4
                 vv
clus              UNTREATED PRIMARY (DE NOVO) GBM
  PRKCD MUTATED                                 3
  PRKCD WILD-TYPE                             262
D18V6, multiclass
                                 clus
vv                                PRKCD MUTATED PRKCD WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)               0              11
  TREATED PRIMARY GBM                         0               4
  UNTREATED PRIMARY (DE NOVO) GBM             3             262
[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"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRKCD MUTATED       0                         1     2
  PRKCD WILD-TYPE     5                        16   250
D18V7, multiclass
                           clus
vv                          PRKCD MUTATED PRKCD WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             1              16
  WHITE                                 2             250
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                 cls
clus                0   1
  PRKCD MUTATED     0   2
  PRKCD WILD-TYPE   3 220
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      0    2
  PRKCD WILD-TYPE    3  220
                        clus
vv                       PRKCD MUTATED PRKCD WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             2             220
[1] 2 2
[1] FALSE

Clustering(19) Variable = TP63 MUTATION ANALYSIS
D19V1, survival
                sevent
clus2              0   1
  TP63 MUTATED     3   3
  TP63 WILD-TYPE  56 215
  TP63 MUTATED TP63 WILD-TYPE 
             6            271 
  TP63 MUTATED TP63 WILD-TYPE 
             3            215 
$`TP63 MUTATED`
TCGA-06-5858 TCGA-19-5960 TCGA-32-1977 TCGA-74-6575 TCGA-06-0744 TCGA-81-5910 
        6.15        14.96         0.10        20.91        46.88         1.61 

$`TP63 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 
        4.77         4.96        15.35        22.19        15.22        10.95 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 
       34.92        14.53        14.93         3.22         2.04        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 
        0.95        23.05        13.78         2.89         1.38        58.78 
TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 
       40.96        17.85         7.63         7.17        17.49         0.39 
TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 
        3.42        29.03        25.38         5.06         9.67         4.87 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 
        7.53         0.16         4.08        24.23         7.00         4.50 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 
        1.78        14.07        16.80        13.87         9.40         8.88 
TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       18.97         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       16.77        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 TCGA-32-1979 
        2.53         1.22         0.66         4.77        15.39        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        1.18         4.67        12.69        16.93        12.23        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.02        15.95         8.84        22.78        25.18        21.14 
TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       20.32         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6577 
       11.84         0.20        15.12        12.46         3.45         4.34 
TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 
       14.33         7.50         4.80         4.54        17.59         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.65         9.17        47.93         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29         2.70        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 
        5.03        23.90        34.45        18.64        36.20         7.63 
TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 
        4.73         2.83        14.73         2.50        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 
       15.45        20.32         2.70         6.15        20.38         6.94 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 
       22.72        33.67        12.95        25.35        26.70        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 
        0.20        10.29         2.20         2.33        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 
       13.94        10.45         3.19        10.82        10.65         5.85 
TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 
       11.41        19.66         3.29         4.47         3.22        88.14 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 
       69.90        73.84        44.58        15.42        38.96         7.40 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 
        0.53        15.02        24.16         0.72        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
       20.42        48.69        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0745 TCGA-06-0747 
        2.10        23.57        14.20        26.40         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 
        2.70         0.92        43.46        46.19         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 
       16.57        20.78        26.76        13.61         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 
        4.37         0.43        31.50         7.79         5.39       120.56 
TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 
        7.36        18.02        14.73        12.99        34.92        26.66 
TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 
        3.65        10.62         2.24        11.24         1.35         5.39 
TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 
       28.93         0.79        13.78        50.53         3.91        31.33 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 
       14.86         5.49         1.58         7.92         2.33         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        23.44        11.01        13.64         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5911 
       12.76         5.42        11.38         5.42         3.75        17.72 
TCGA-87-5896 
       26.30 

  TP63 MUTATED TP63 WILD-TYPE 
          0.10           0.16 
  TP63 MUTATED TP63 WILD-TYPE 
         46.88         120.56 
  TP63 MUTATED TP63 WILD-TYPE 
        10.555         11.510 
[1] "0.1 - 46.9 (10.6)"  "0.2 - 120.6 (11.5)"
[1] "hr=" "1.8"
D19V2, continuous
D19V3, binary
                cls
clus               0   1
  TP63 MUTATED     3   3
  TP63 WILD-TYPE  98 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED      3    3
  TP63 WILD-TYPE   98  176
        clus
vv       TP63 MUTATED TP63 WILD-TYPE
  FEMALE            3             98
  MALE              3            176
[1] 2 2
[1] FALSE
D19V4, binary
                cls
clus               0   1
  TP63 MUTATED     1   4
  TP63 WILD-TYPE  45 213
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED      1    4
  TP63 WILD-TYPE   45  213
     clus
vv    TP63 MUTATED TP63 WILD-TYPE
  NO             1             45
  YES            4            213
[1] 2 2
[1] FALSE
D19V5, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  TP63 MUTATED                               0                   0
  TP63 WILD-TYPE                            11                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  TP63 MUTATED                                 6
  TP63 WILD-TYPE                             259
D19V6, multiclass
                                 clus
vv                                TP63 MUTATED TP63 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              0             11
  TREATED PRIMARY GBM                        0              4
  UNTREATED PRIMARY (DE NOVO) GBM            6            259
[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"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP63 MUTATED       0                         0     5
  TP63 WILD-TYPE     5                        17   247
D19V7, multiclass
                           clus
vv                          TP63 MUTATED TP63 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0             17
  WHITE                                5            247
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                cls
clus               0   1
  TP63 MUTATED     1   3
  TP63 WILD-TYPE   2 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP63 MUTATED      1    3
  TP63 WILD-TYPE    2  219
                        clus
vv                       TP63 MUTATED TP63 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO            3            219
[1] 2 2
[1] FALSE

Clustering(20) Variable = PDGFRA MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2                0   1
  PDGFRA MUTATED     1  10
  PDGFRA WILD-TYPE  58 208
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              11              266 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              10              208 
$`PDGFRA MUTATED`
TCGA-14-0740 TCGA-19-1390 TCGA-19-2631 TCGA-27-1831 TCGA-02-0047 TCGA-06-0174 
       11.97        25.38         7.00        16.60        14.73         3.22 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0241 TCGA-06-2559 TCGA-26-5134 
        0.53        15.02        48.69         4.93         5.49 

$`PDGFRA WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 
        1.55         4.77         4.96        15.35        22.19        15.22 
TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 
        0.95        23.05        13.78         2.89         1.38        58.78 
TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 
       40.96        17.85         7.63         7.17        17.49         0.39 
TCGA-14-4157 TCGA-16-1045 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 
        3.42        29.03         5.06         9.67         4.87         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 
        0.16         4.08        24.23         4.50         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
        8.02        18.90         4.73        12.10         1.78        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 
       16.80        14.96        13.87         9.40         8.88        18.97 
TCGA-27-1830 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
        5.06         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        18.08        16.77        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 
        7.59         2.86        14.40        15.78         2.53         1.22 
TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 
        0.66         4.77        15.39         0.10        19.50         1.18 
TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
        4.67        12.69        16.93        12.23        20.78        15.02 
TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 
       15.95         8.84        22.78        25.18        21.14        20.32 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        0.20        15.12        12.46         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 
       14.33         7.50         4.80         4.54        17.59         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.65         9.17        47.93         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29         2.70        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 
        5.03        23.90        34.45        18.64        36.20         7.63 
TCGA-02-0003 TCGA-02-0033 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
        4.73         2.83         2.50        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 
       20.32         2.70         6.15        20.38         6.94        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 
       33.67        12.95        25.35        26.70        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.29         2.20         2.33        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 
       10.45         3.19        10.82        10.65         5.85        11.41 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0178 TCGA-06-0184 TCGA-06-0185 
       19.66         3.29         4.47        88.14        69.90        73.84 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0216 TCGA-06-0219 
       44.58        15.42        38.96         7.40        24.16         0.72 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
       13.64        13.32        20.42        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 
        7.17        40.41        16.57        20.78        26.76        13.61 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
        1.08        12.49        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 
       16.64         4.37         0.43        31.50         7.79         5.39 
TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
      120.56         7.36        18.02        14.73        12.99        34.92 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 
       26.66         3.65        10.62         2.24        11.24         1.35 
TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-16-0846 
        5.39        28.93         0.79        13.78        50.53         3.91 
TCGA-26-1442 TCGA-26-5133 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 
       31.33        14.86         1.58         7.92         2.33         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        23.44        11.01        13.64         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 
       12.76         5.42        11.38         5.42         3.75         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

  PDGFRA MUTATED PDGFRA WILD-TYPE 
            0.53             0.10 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
           48.69           120.56 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
           11.97            11.46 
[1] "0.5 - 48.7 (12.0)"  "0.1 - 120.6 (11.5)"
[1] "hr=" "1.1"
D20V2, continuous
D20V3, binary
                  cls
clus                 0   1
  PDGFRA MUTATED     4   7
  PDGFRA WILD-TYPE  97 172
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED      4    7
  PDGFRA WILD-TYPE   97  172
        clus
vv       PDGFRA MUTATED PDGFRA WILD-TYPE
  FEMALE              4               97
  MALE                7              172
[1] 2 2
[1] FALSE
D20V4, binary
                  cls
clus                 0   1
  PDGFRA MUTATED     3   8
  PDGFRA WILD-TYPE  43 209
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED      3    8
  PDGFRA WILD-TYPE   43  209
     clus
vv    PDGFRA MUTATED PDGFRA WILD-TYPE
  NO               3               43
  YES              8              209
[1] 2 2
[1] FALSE
D20V5, continuous
                  vv
clus               GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  PDGFRA MUTATED                               0                   0
  PDGFRA WILD-TYPE                            11                   4
                  vv
clus               UNTREATED PRIMARY (DE NOVO) GBM
  PDGFRA MUTATED                                11
  PDGFRA WILD-TYPE                             254
D20V6, multiclass
                                 clus
vv                                PDGFRA MUTATED PDGFRA WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                0               11
  TREATED PRIMARY GBM                          0                4
  UNTREATED PRIMARY (DE NOVO) GBM             11              254
[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"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PDGFRA MUTATED       0                         0    11
  PDGFRA WILD-TYPE     5                        17   241
D20V7, multiclass
                           clus
vv                          PDGFRA MUTATED PDGFRA WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0               17
  WHITE                                 11              241
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                  cls
clus                 0   1
  PDGFRA MUTATED     0  10
  PDGFRA WILD-TYPE   3 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED      0   10
  PDGFRA WILD-TYPE    3  212
                        clus
vv                       PDGFRA MUTATED PDGFRA WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO             10              212
[1] 2 2
[1] FALSE

Clustering(21) Variable = CHD8 MUTATION ANALYSIS
D21V1, survival
                sevent
clus2              0   1
  CHD8 MUTATED     3   5
  CHD8 WILD-TYPE  56 213
  CHD8 MUTATED CHD8 WILD-TYPE 
             8            269 
  CHD8 MUTATED CHD8 WILD-TYPE 
             5            213 
$`CHD8 MUTATED`
TCGA-06-5410 TCGA-06-5413 TCGA-19-5959 TCGA-32-1982 TCGA-06-1804 TCGA-06-2559 
        3.55         8.81        16.80         4.67        13.61         4.93 
TCGA-26-1442 TCGA-26-6174 
       31.33         2.33 

$`CHD8 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5411 TCGA-06-5412 TCGA-06-5414 
        1.48        15.32        11.74         8.35         4.54         8.98 
TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.55         5.10         2.73         3.75         6.15         4.57 
TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 
        5.23         8.32        12.85         4.77         1.55         4.77 
TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
        4.96        15.35        22.19        15.22        10.95        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 
       14.53        14.93         3.22         2.04        11.97         0.95 
TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 
       23.05        13.78         2.89         1.38        58.78        40.96 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 
       17.85         7.63         7.17        17.49         0.39         3.42 
TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 
       29.03        25.38         5.06         9.67         4.87         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 
        0.16         4.08        24.23         7.00         4.50         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5958 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 
       14.07        14.96        13.87         9.40         8.88        18.97 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        14.04        11.51        24.76        18.08        16.77 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 
       16.08         7.59         2.86        14.40        15.78         2.53 
TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 
        1.22         0.66         4.77        15.39         0.10        19.50 
TCGA-32-1980 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
        1.18        12.69        16.93        12.23        20.78        15.02 
TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 
       15.95         8.84        22.78        25.18        21.14        20.32 
TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 
        3.72        12.59        19.86        10.85        19.23         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 
        0.20        15.12        12.46         3.45        20.91         4.34 
TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 
       14.33         7.50         4.80         4.54        17.59         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.65         9.17        47.93         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29         2.70        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 
        5.03        23.90        34.45        18.64        36.20         7.63 
TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 
        4.73         2.83        14.73         2.50        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 
       15.45        20.32         2.70         6.15        20.38         6.94 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 
       22.72        33.67        12.95        25.35        26.70        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 
        0.20        10.29         2.20         2.33        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 
       13.94        10.45         3.19        10.82        10.65         5.85 
TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 
       11.41        19.66         3.29         4.47         3.22        88.14 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 
       69.90        73.84        44.58        15.42        38.96         7.40 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 
        0.53        15.02        24.16         0.72        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
       20.42        48.69        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.10        23.57        14.20        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 
        2.70         2.70         0.92        43.46        46.19         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-2557 TCGA-06-2558 
       40.41        16.57        20.78        26.76         1.08        12.49 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 
       17.65        12.56        30.64         5.95        16.64         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 
        0.43        31.50         7.79         5.39       120.56         7.36 
TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 
       18.02        14.73        12.99        34.92        26.66         3.65 
TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 
       10.62         2.24        11.24         1.35         5.39        28.93 
TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-26-5133 TCGA-26-5134 
        0.79        13.78        50.53         3.91        14.86         5.49 
TCGA-26-5139 TCGA-26-6173 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        1.58         7.92         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 
       13.64         5.16        22.68        12.76         5.42        11.38 
TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        5.42         3.75         1.61        17.72        26.30 

  CHD8 MUTATED CHD8 WILD-TYPE 
          2.33           0.10 
  CHD8 MUTATED CHD8 WILD-TYPE 
         31.33         120.56 
  CHD8 MUTATED CHD8 WILD-TYPE 
          6.87          11.74 
[1] "2.3 - 31.3 (6.9)"   "0.1 - 120.6 (11.7)"
[1] "hr=" "1.1"
D21V2, continuous
D21V3, binary
                cls
clus               0   1
  CHD8 MUTATED     5   3
  CHD8 WILD-TYPE  96 176
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD8 MUTATED      5    3
  CHD8 WILD-TYPE   96  176
        clus
vv       CHD8 MUTATED CHD8 WILD-TYPE
  FEMALE            5             96
  MALE              3            176
[1] 2 2
[1] FALSE
D21V4, binary
                cls
clus               0   1
  CHD8 MUTATED     2   5
  CHD8 WILD-TYPE  44 212
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD8 MUTATED      2    5
  CHD8 WILD-TYPE   44  212
     clus
vv    CHD8 MUTATED CHD8 WILD-TYPE
  NO             2             44
  YES            5            212
[1] 2 2
[1] FALSE
D21V5, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  CHD8 MUTATED                               0                   0
  CHD8 WILD-TYPE                            11                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  CHD8 MUTATED                                 8
  CHD8 WILD-TYPE                             257
D21V6, multiclass
                                 clus
vv                                CHD8 MUTATED CHD8 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              0             11
  TREATED PRIMARY GBM                        0              4
  UNTREATED PRIMARY (DE NOVO) GBM            8            257
[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"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CHD8 MUTATED       0                         0     8
  CHD8 WILD-TYPE     5                        17   244
D21V7, multiclass
                           clus
vv                          CHD8 MUTATED CHD8 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0             17
  WHITE                                8            244
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                cls
clus               0   1
  CHD8 MUTATED     0   8
  CHD8 WILD-TYPE   3 214
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD8 MUTATED      0    8
  CHD8 WILD-TYPE    3  214
                        clus
vv                       CHD8 MUTATED CHD8 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            8            214
[1] 2 2
[1] FALSE

Clustering(22) Variable = IL4R MUTATION ANALYSIS
D22V1, survival
                sevent
clus2              0   1
  IL4R MUTATED     1   7
  IL4R WILD-TYPE  58 211
  IL4R MUTATED IL4R WILD-TYPE 
             8            269 
  IL4R MUTATED IL4R WILD-TYPE 
             7            211 
$`IL4R MUTATED`
TCGA-06-6388 TCGA-06-6698 TCGA-14-0790 TCGA-27-1833 TCGA-32-1982 TCGA-41-5651 
        5.23         4.77        13.78        24.23         4.67        15.12 
TCGA-14-0813 TCGA-16-0846 
        1.35         3.91 

$`IL4R WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 TCGA-06-6700 
        6.15         4.57         8.32        12.85         1.55         4.77 
TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 
        4.96        15.35        22.19        15.22        10.95        34.92 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 
       14.53        14.93         3.22         2.04        11.97         0.95 
TCGA-14-0786 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 
       23.05         2.89         1.38        58.78        40.96        17.85 
TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 TCGA-16-1045 
        7.63         7.17        17.49         0.39         3.42        29.03 
TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 
       25.38         5.06         9.67         4.87         7.53         0.16 
TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 
        4.08        24.23         7.00         4.50         6.64        17.19 
TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 
        8.02        18.90         4.73        12.10         1.78        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 
       16.80        14.96        13.87         9.40         8.88        18.97 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
        5.06        16.60         9.86        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        18.08        16.77        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 
        7.59         2.86        14.40        15.78         2.53         1.22 
TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 
        0.66         4.77        15.39         0.10        19.50         1.18 
TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       12.69        16.93        12.23        20.78        15.02        15.95 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 
        8.84        22.78        25.18        21.14        20.32         3.72 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       12.59        19.86        10.85        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
        8.94         9.53         0.99         4.44        11.84         0.20 
TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 
       12.46         3.45        20.91         4.34        14.33         7.50 
TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        4.80         4.54        17.59         3.09         3.65         9.17 
TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 
       47.93         2.53        36.85        16.70         3.29         2.70 
TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 
       17.06         8.35        20.98         4.83         5.03        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 TCGA-02-0033 
       34.45        18.64        36.20         7.63         4.73         2.83 
TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
       14.73         2.50        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 
        2.70         6.15        20.38         6.94        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       12.95        25.35        26.70        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        2.20         2.33        46.59        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 TCGA-06-0168 
        3.19        10.82        10.65         5.85        11.41        19.66 
TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 TCGA-06-0184 TCGA-06-0185 
        3.29         4.47         3.22        88.14        69.90        73.84 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0213 TCGA-06-0214 
       44.58        15.42        38.96         7.40         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       24.16         0.72        13.64        13.32        20.42        48.69 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.62         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 
        0.92        43.46        46.19         7.17        40.41        16.57 
TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 
       20.78        26.76        13.61         1.08        12.49         4.93 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 
       17.65        12.56        30.64         5.95        16.64         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 
        0.43        31.50         7.79         5.39       120.56         7.36 
TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 
       18.02        14.73        12.99        34.92        26.66         3.65 
TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 
       10.62         2.24        11.24         5.39        28.93         0.79 
TCGA-15-0742 TCGA-15-1444 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 
       13.78        50.53        31.33        14.86         5.49         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        7.92         2.33         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 
       13.64         5.16        22.68        12.76         5.42        11.38 
TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        5.42         3.75         1.61        17.72        26.30 

  IL4R MUTATED IL4R WILD-TYPE 
          1.35           0.10 
  IL4R MUTATED IL4R WILD-TYPE 
         24.23         120.56 
  IL4R MUTATED IL4R WILD-TYPE 
          5.00          11.74 
[1] "1.4 - 24.2 (5.0)"   "0.1 - 120.6 (11.7)"
[1] "hr=" "1.7"
D22V2, continuous
D22V3, binary
                cls
clus               0   1
  IL4R MUTATED     6   2
  IL4R WILD-TYPE  95 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL4R MUTATED      6    2
  IL4R WILD-TYPE   95  177
        clus
vv       IL4R MUTATED IL4R WILD-TYPE
  FEMALE            6             95
  MALE              2            177
[1] 2 2
[1] FALSE
D22V4, binary
                cls
clus               0   1
  IL4R MUTATED     2   5
  IL4R WILD-TYPE  44 212
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL4R MUTATED      2    5
  IL4R WILD-TYPE   44  212
     clus
vv    IL4R MUTATED IL4R WILD-TYPE
  NO             2             44
  YES            5            212
[1] 2 2
[1] FALSE
D22V5, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  IL4R MUTATED                               0                   0
  IL4R WILD-TYPE                            11                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  IL4R MUTATED                                 8
  IL4R WILD-TYPE                             257
D22V6, multiclass
                                 clus
vv                                IL4R MUTATED IL4R WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              0             11
  TREATED PRIMARY GBM                        0              4
  UNTREATED PRIMARY (DE NOVO) GBM            8            257
[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"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IL4R MUTATED       0                         1     7
  IL4R WILD-TYPE     5                        16   245
D22V7, multiclass
                           clus
vv                          IL4R MUTATED IL4R WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            1             16
  WHITE                                7            245
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                cls
clus               0   1
  IL4R MUTATED     0   6
  IL4R WILD-TYPE   3 216
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL4R MUTATED      0    6
  IL4R WILD-TYPE    3  216
                        clus
vv                       IL4R MUTATED IL4R WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            6            216
[1] 2 2
[1] FALSE

Clustering(23) Variable = REN MUTATION ANALYSIS
D23V1, survival
               sevent
clus2             0   1
  REN MUTATED     1   4
  REN WILD-TYPE  58 214
  REN MUTATED REN WILD-TYPE 
            5           272 
  REN MUTATED REN WILD-TYPE 
            4           214 
$`REN MUTATED`
TCGA-06-5411 TCGA-32-2495 TCGA-41-3392 TCGA-74-6577 TCGA-76-6662 
        8.35        15.02         0.99         4.34        34.45 

$`REN WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 
        1.48        15.32        11.74         3.55         4.54         8.81 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.98         8.55         5.10         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 
        4.77         4.96        15.35        22.19        15.22        10.95 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 
       34.92        14.53        14.93         3.22         2.04        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 
        0.95        23.05        13.78         2.89         1.38        58.78 
TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 
       40.96        17.85         7.63         7.17        17.49         0.39 
TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 
        3.42        29.03        25.38         5.06         9.67         4.87 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 
        7.53         0.16         4.08        24.23         7.00         4.50 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 
        1.78        14.07        16.80        14.96        13.87         9.40 
TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        8.88        18.97         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       18.08        16.77        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 
       15.78         2.53         1.22         0.66         4.77        15.39 
TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 
        0.10        19.50         1.18         4.67        12.69        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       12.23        20.78        15.95         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       21.14        20.32         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3393 
       19.23         0.85        13.35         8.94         9.53         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
       11.84         0.20        15.12        12.46         3.45        20.91 
TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 
       14.33         7.50         4.80         4.54        17.59         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.65         9.17        47.93         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29         2.70        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 
        5.03        23.90        18.64        36.20         7.63         4.73 
TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
        2.83        14.73         2.50        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 
       20.32         2.70         6.15        20.38         6.94        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 
       33.67        12.95        25.35        26.70        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.29         2.20         2.33        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 
       10.45         3.19        10.82        10.65         5.85        11.41 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 TCGA-06-0184 
       19.66         3.29         4.47         3.22        88.14        69.90 
TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0213 
       73.84        44.58        15.42        38.96         7.40         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       15.02        24.16         0.72        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       48.69        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 
        2.70         0.92        43.46        46.19         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 
       16.57        20.78        26.76        13.61         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 
        4.37         0.43        31.50         7.79         5.39       120.56 
TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 
        7.36        18.02        14.73        12.99        34.92        26.66 
TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 
        3.65        10.62         2.24        11.24         1.35         5.39 
TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 
       28.93         0.79        13.78        50.53         3.91        31.33 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 
       14.86         5.49         1.58         7.92         2.33         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        23.44        11.01        13.64         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 
       12.76         5.42        11.38         5.42         3.75         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

  REN MUTATED REN WILD-TYPE 
         0.99          0.10 
  REN MUTATED REN WILD-TYPE 
        34.45        120.56 
  REN MUTATED REN WILD-TYPE 
        8.350        11.625 
[1] "1.0 - 34.5 (8.3)"   "0.1 - 120.6 (11.6)"
[1] "hr=" "1.2"
D23V2, continuous
D23V3, binary
               cls
clus              0   1
  REN MUTATED     1   4
  REN WILD-TYPE 100 175
[1] "tbl2"
               cls
clus            [,1] [,2]
  REN MUTATED      1    4
  REN WILD-TYPE  100  175
        clus
vv       REN MUTATED REN WILD-TYPE
  FEMALE           1           100
  MALE             4           175
[1] 2 2
[1] FALSE
D23V4, binary
               cls
clus              0   1
  REN MUTATED     1   4
  REN WILD-TYPE  45 213
[1] "tbl2"
               cls
clus            [,1] [,2]
  REN MUTATED      1    4
  REN WILD-TYPE   45  213
     clus
vv    REN MUTATED REN WILD-TYPE
  NO            1            45
  YES           4           213
[1] 2 2
[1] FALSE
D23V5, continuous
               vv
clus            GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  REN MUTATED                               0                   1
  REN WILD-TYPE                            11                   3
               vv
clus            UNTREATED PRIMARY (DE NOVO) GBM
  REN MUTATED                                 4
  REN WILD-TYPE                             261
D23V6, multiclass
                                 clus
vv                                REN MUTATED REN WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)             0            11
  TREATED PRIMARY GBM                       1             3
  UNTREATED PRIMARY (DE NOVO) GBM           4           261
[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"
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  REN MUTATED       0                         0     4
  REN WILD-TYPE     5                        17   248
D23V7, multiclass
                           clus
vv                          REN MUTATED REN WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0            17
  WHITE                               4           248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
               cls
clus              0   1
  REN MUTATED     0   4
  REN WILD-TYPE   3 218
[1] "tbl2"
               cls
clus            [,1] [,2]
  REN MUTATED      0    4
  REN WILD-TYPE    3  218
                        clus
vv                       REN MUTATED REN WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           4           218
[1] 2 2
[1] FALSE

Clustering(24) Variable = CD209 MUTATION ANALYSIS
D24V1, survival
                 sevent
clus2               0   1
  CD209 MUTATED     2   3
  CD209 WILD-TYPE  57 215
  CD209 MUTATED CD209 WILD-TYPE 
              5             272 
  CD209 MUTATED CD209 WILD-TYPE 
              3             215 
$`CD209 MUTATED`
TCGA-06-6698 TCGA-19-4068 TCGA-41-2571 TCGA-76-4931 TCGA-06-0650 
        4.77         4.50         0.85         9.17        23.57 

$`CD209 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6699 
        6.15         4.57         5.23         8.32        12.85         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 
        4.77         4.96        15.35        22.19        15.22        10.95 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 
       34.92        14.53        14.93         3.22         2.04        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 
        0.95        23.05        13.78         2.89         1.38        58.78 
TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 
       40.96        17.85         7.63         7.17        17.49         0.39 
TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 
        3.42        29.03        25.38         5.06         9.67         4.87 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-5947 
        7.53         0.16         4.08        24.23         7.00         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 
       14.07        16.80        14.96        13.87         9.40         8.88 
TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       18.97         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       16.77        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 TCGA-32-1977 
        2.53         1.22         0.66         4.77        15.39         0.10 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 
       19.50         1.18         4.67        12.69        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       20.78        15.02        15.95         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       21.14        20.32         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
       19.23        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
       11.84         0.20        15.12        12.46         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 
        4.34        14.33         7.50         4.80         4.54        17.59 
TCGA-76-4928 TCGA-76-4929 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.09         3.65        47.93         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29         2.70        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 
        5.03        23.90        34.45        18.64        36.20         7.63 
TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 
        4.73         2.83        14.73         2.50        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 
       15.45        20.32         2.70         6.15        20.38         6.94 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 
       22.72        33.67        12.95        25.35        26.70        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 
        0.20        10.29         2.20         2.33        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 
       13.94        10.45         3.19        10.82        10.65         5.85 
TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 
       11.41        19.66         3.29         4.47         3.22        88.14 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 
       69.90        73.84        44.58        15.42        38.96         7.40 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 
        0.53        15.02        24.16         0.72        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
       20.42        48.69        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        2.10        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 
        2.70         0.92        43.46        46.19         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 
       16.57        20.78        26.76        13.61         1.08        12.49 
TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 
        4.93        17.65        12.56        30.64         5.95        16.64 
TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 
        4.37         0.43        31.50         7.79         5.39       120.56 
TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 
        7.36        18.02        14.73        12.99        34.92        26.66 
TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 
        3.65        10.62         2.24        11.24         1.35         5.39 
TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 
       28.93         0.79        13.78        50.53         3.91        31.33 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 
       14.86         5.49         1.58         7.92         2.33         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        23.44        11.01        13.64         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 
       12.76         5.42        11.38         5.42         3.75         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

  CD209 MUTATED CD209 WILD-TYPE 
           0.85            0.10 
  CD209 MUTATED CD209 WILD-TYPE 
          23.57          120.56 
  CD209 MUTATED CD209 WILD-TYPE 
          4.770          11.755 
[1] "0.8 - 23.6 (4.8)"   "0.1 - 120.6 (11.8)"
[1] "hr=" "1.3"
D24V2, continuous
D24V3, binary
                 cls
clus                0   1
  CD209 MUTATED     4   1
  CD209 WILD-TYPE  97 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD209 MUTATED      4    1
  CD209 WILD-TYPE   97  178
        clus
vv       CD209 MUTATED CD209 WILD-TYPE
  FEMALE             4              97
  MALE               1             178
[1] 2 2
[1] FALSE
D24V4, binary
                 cls
clus                0   1
  CD209 MUTATED     1   4
  CD209 WILD-TYPE  45 213
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD209 MUTATED      1    4
  CD209 WILD-TYPE   45  213
     clus
vv    CD209 MUTATED CD209 WILD-TYPE
  NO              1              45
  YES             4             213
[1] 2 2
[1] FALSE
D24V5, continuous
                 vv
clus              GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  CD209 MUTATED                               0                   0
  CD209 WILD-TYPE                            11                   4
                 vv
clus              UNTREATED PRIMARY (DE NOVO) GBM
  CD209 MUTATED                                 5
  CD209 WILD-TYPE                             260
D24V6, multiclass
                                 clus
vv                                CD209 MUTATED CD209 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)               0              11
  TREATED PRIMARY GBM                         0               4
  UNTREATED PRIMARY (DE NOVO) GBM             5             260
[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"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD209 MUTATED       0                         0     5
  CD209 WILD-TYPE     5                        17   247
D24V7, multiclass
                           clus
vv                          CD209 MUTATED CD209 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0              17
  WHITE                                 5             247
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                 cls
clus                0   1
  CD209 MUTATED     0   4
  CD209 WILD-TYPE   3 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD209 MUTATED      0    4
  CD209 WILD-TYPE    3  218
                        clus
vv                       CD209 MUTATED CD209 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             218
[1] 2 2
[1] FALSE

Clustering(25) Variable = FBN3 MUTATION ANALYSIS
D25V1, survival
                sevent
clus2              0   1
  FBN3 MUTATED     4   7
  FBN3 WILD-TYPE  55 211
  FBN3 MUTATED FBN3 WILD-TYPE 
            11            266 
  FBN3 MUTATED FBN3 WILD-TYPE 
             7            211 
$`FBN3 MUTATED`
TCGA-06-6699 TCGA-19-2619 TCGA-27-1838 TCGA-32-2495 TCGA-32-4210 TCGA-76-6657 
        1.55         9.67        11.51        15.02         3.72         5.03 
TCGA-06-0174 TCGA-06-2564 TCGA-28-2513 TCGA-28-5220 TCGA-81-5910 
        3.22         5.95         7.30        12.76         1.61 

$`FBN3 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 
        4.77         4.96        15.35        22.19        15.22        10.95 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 
       34.92        14.53        14.93         3.22         2.04        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 
        0.95        23.05        13.78         2.89         1.38        58.78 
TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 
       40.96        17.85         7.63         7.17        17.49         0.39 
TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2620 TCGA-19-2623 
        3.42        29.03        25.38         5.06         4.87         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 
        0.16         4.08        24.23         7.00         4.50         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 
       14.07        16.80        14.96        13.87         9.40         8.88 
TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       18.97         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       21.30        30.05        14.04        24.76        18.08        16.77 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 
       16.08         7.59         2.86        14.40        15.78         2.53 
TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 
        1.22         0.66         4.77        15.39         0.10        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        1.18         4.67        12.69        16.93        12.23        20.78 
TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 
       15.95         8.84        22.78        25.18        21.14        20.32 
TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 
       12.59        19.86        10.85        19.23         0.85        13.35 
TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 
        8.94         9.53         0.99         4.44        11.84         0.20 
TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
       15.12        12.46         3.45        20.91         4.34        14.33 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 
        7.50         4.80         4.54        17.59         3.09         3.65 
TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        9.17        47.93         2.53        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6661 
        2.70        17.06         8.35        20.98         4.83        23.90 
TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 TCGA-02-0033 
       34.45        18.64        36.20         7.63         4.73         2.83 
TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 
       14.73         2.50        12.92        15.32        15.45        20.32 
TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 
        2.70         6.15        20.38         6.94        22.72        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       12.95        25.35        26.70        11.90         0.20        10.29 
TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        2.20         2.33        46.59        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 TCGA-06-0168 
        3.19        10.82        10.65         5.85        11.41        19.66 
TCGA-06-0169 TCGA-06-0173 TCGA-06-0178 TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 
        3.29         4.47        88.14        69.90        73.84        44.58 
TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
       15.42        38.96         7.40         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 
        0.72        13.64        13.32        20.42        48.69        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 
        5.75         5.75         9.80         2.10        23.57        14.20 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 
       26.40        46.88         7.86         2.70         2.70         0.92 
TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 
       43.46        46.19         7.17        40.41        16.57        20.78 
TCGA-06-0939 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 
       26.76        13.61         1.08        12.49         4.93        17.65 
TCGA-06-2562 TCGA-06-2563 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
       12.56        30.64        16.64         4.37         0.43        31.50 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 
        7.79         5.39       120.56         7.36        18.02        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 
       12.99        34.92        26.66         3.65        10.62         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 
       11.24         1.35         5.39        28.93         0.79        13.78 
TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 
       50.53         3.91        31.33        14.86         5.49         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        7.92         2.33         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 
        5.16        22.68         5.42        11.38         5.42         3.75 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

  FBN3 MUTATED FBN3 WILD-TYPE 
          1.55           0.10 
  FBN3 MUTATED FBN3 WILD-TYPE 
         15.02         120.56 
  FBN3 MUTATED FBN3 WILD-TYPE 
          5.95          11.87 
[1] "1.6 - 15.0 (6.0)"   "0.1 - 120.6 (11.9)"
[1] "hr=" "1.9"
D25V2, continuous
D25V3, binary
                cls
clus               0   1
  FBN3 MUTATED     5   6
  FBN3 WILD-TYPE  96 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN3 MUTATED      5    6
  FBN3 WILD-TYPE   96  173
        clus
vv       FBN3 MUTATED FBN3 WILD-TYPE
  FEMALE            5             96
  MALE              6            173
[1] 2 2
[1] FALSE
D25V4, binary
                cls
clus               0   1
  FBN3 MUTATED     1   9
  FBN3 WILD-TYPE  45 208
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN3 MUTATED      1    9
  FBN3 WILD-TYPE   45  208
     clus
vv    FBN3 MUTATED FBN3 WILD-TYPE
  NO             1             45
  YES            9            208
[1] 2 2
[1] FALSE
D25V5, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  FBN3 MUTATED                               0                   1
  FBN3 WILD-TYPE                            11                   3
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  FBN3 MUTATED                                10
  FBN3 WILD-TYPE                             255
D25V6, multiclass
                                 clus
vv                                FBN3 MUTATED FBN3 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              0             11
  TREATED PRIMARY GBM                        1              3
  UNTREATED PRIMARY (DE NOVO) GBM           10            255
[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"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FBN3 MUTATED       0                         1    10
  FBN3 WILD-TYPE     5                        16   242
D25V7, multiclass
                           clus
vv                          FBN3 MUTATED FBN3 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            1             16
  WHITE                               10            242
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                cls
clus               0   1
  FBN3 MUTATED     0   9
  FBN3 WILD-TYPE   3 213
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN3 MUTATED      0    9
  FBN3 WILD-TYPE    3  213
                        clus
vv                       FBN3 MUTATED FBN3 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            9            213
[1] 2 2
[1] FALSE

Clustering(26) Variable = MMP13 MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2               0   1
  MMP13 MUTATED     1   4
  MMP13 WILD-TYPE  58 214
  MMP13 MUTATED MMP13 WILD-TYPE 
              5             272 
  MMP13 MUTATED MMP13 WILD-TYPE 
              4             214 
$`MMP13 MUTATED`
TCGA-06-6699 TCGA-12-3652 TCGA-27-2527 TCGA-76-4925 TCGA-12-0688 
        1.55        34.92        14.40         4.80        26.66 

$`MMP13 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 
        4.77         4.96        15.35        22.19        15.22        10.95 
TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 
       14.53        14.93         3.22         2.04        11.97         0.95 
TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 
       23.05        13.78         2.89         1.38        58.78        40.96 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 
       17.85         7.63         7.17        17.49         0.39         3.42 
TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 
       29.03        25.38         5.06         9.67         4.87         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 
        0.16         4.08        24.23         7.00         4.50         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 
       14.07        16.80        14.96        13.87         9.40         8.88 
TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       18.97         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1747 
       16.77        16.08         7.59         2.86        15.78         2.53 
TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 
        1.22         0.66         4.77        15.39         0.10        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        1.18         4.67        12.69        16.93        12.23        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.02        15.95         8.84        22.78        25.18        21.14 
TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 
       20.32         3.72        12.59        19.86        10.85        19.23 
TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 
        0.85        13.35         8.94         9.53         0.99         4.44 
TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 
       11.84         0.20        15.12        12.46         3.45        20.91 
TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 
        4.34        14.33         7.50         4.54        17.59         3.09 
TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        3.65         9.17        47.93         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 
        3.29         2.70        17.06         8.35        20.98         4.83 
TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 
        5.03        23.90        34.45        18.64        36.20         7.63 
TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 
        4.73         2.83        14.73         2.50        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 
       15.45        20.32         2.70         6.15        20.38         6.94 
TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 
       22.72        33.67        12.95        25.35        26.70        11.90 
TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 
        0.20        10.29         2.20         2.33        46.59        12.33 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 
       13.94        10.45         3.19        10.82        10.65         5.85 
TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 
       11.41        19.66         3.29         4.47         3.22        88.14 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 
       69.90        73.84        44.58        15.42        38.96         7.40 
TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 
        0.53        15.02        24.16         0.72        13.64        13.32 
TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 
       20.42        48.69        12.62         5.75         5.75         9.80 
TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 
        2.10        23.57        14.20        26.40        46.88         7.86 
TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 
        2.70         2.70         0.92        43.46        46.19         7.17 
TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-2557 
       40.41        16.57        20.78        26.76        13.61         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 
       16.64         4.37         0.43        31.50         7.79         5.39 
TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
      120.56         7.36        18.02        14.73        12.99        34.92 
TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 
        3.65        10.62         2.24        11.24         1.35         5.39 
TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 
       28.93         0.79        13.78        50.53         3.91        31.33 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 
       14.86         5.49         1.58         7.92         2.33         7.30 
TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 
        5.26        14.93        11.28        17.88        14.53        11.77 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 
       31.27        23.44        11.01        13.64         5.16        22.68 
TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 
       12.76         5.42        11.38         5.42         3.75         1.61 
TCGA-81-5911 TCGA-87-5896 
       17.72        26.30 

  MMP13 MUTATED MMP13 WILD-TYPE 
           1.55            0.10 
  MMP13 MUTATED MMP13 WILD-TYPE 
          34.92          120.56 
  MMP13 MUTATED MMP13 WILD-TYPE 
          14.40           11.46 
[1] "1.6 - 34.9 (14.4)"  "0.1 - 120.6 (11.5)"
[1] "hr=" "1.2"
D26V2, continuous
D26V3, binary
                 cls
clus                0   1
  MMP13 MUTATED     1   4
  MMP13 WILD-TYPE 100 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      1    4
  MMP13 WILD-TYPE  100  175
        clus
vv       MMP13 MUTATED MMP13 WILD-TYPE
  FEMALE             1             100
  MALE               4             175
[1] 2 2
[1] FALSE
D26V4, binary
                 cls
clus                0   1
  MMP13 MUTATED     0   5
  MMP13 WILD-TYPE  46 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      0    5
  MMP13 WILD-TYPE   46  212
     clus
vv    MMP13 MUTATED MMP13 WILD-TYPE
  NO              0              46
  YES             5             212
[1] 2 2
[1] FALSE
D26V5, continuous
                 vv
clus              GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  MMP13 MUTATED                               0                   0
  MMP13 WILD-TYPE                            11                   4
                 vv
clus              UNTREATED PRIMARY (DE NOVO) GBM
  MMP13 MUTATED                                 5
  MMP13 WILD-TYPE                             260
D26V6, multiclass
                                 clus
vv                                MMP13 MUTATED MMP13 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)               0              11
  TREATED PRIMARY GBM                         0               4
  UNTREATED PRIMARY (DE NOVO) GBM             5             260
[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"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MMP13 MUTATED       0                         0     5
  MMP13 WILD-TYPE     5                        17   247
D26V7, multiclass
                           clus
vv                          MMP13 MUTATED MMP13 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0              17
  WHITE                                 5             247
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                 cls
clus                0   1
  MMP13 MUTATED     0   5
  MMP13 WILD-TYPE   3 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      0    5
  MMP13 WILD-TYPE    3  217
                        clus
vv                       MMP13 MUTATED MMP13 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             5             217
[1] 2 2
[1] FALSE

Clustering(27) Variable = TCF12 MUTATION ANALYSIS
D27V1, survival
                 sevent
clus2               0   1
  TCF12 MUTATED     1   3
  TCF12 WILD-TYPE  58 215
  TCF12 MUTATED TCF12 WILD-TYPE 
              4             273 
  TCF12 MUTATED TCF12 WILD-TYPE 
              3             215 
$`TCF12 MUTATED`
TCGA-06-5414 TCGA-19-1790 TCGA-06-0128 TCGA-76-6283 
        8.98         5.06        22.72         5.42 

$`TCF12 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 
        8.81         8.55         5.10         2.73         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 
        4.77         4.96        15.35        22.19        15.22        10.95 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 
       34.92        14.53        14.93         3.22         2.04        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 
        0.95        23.05        13.78         2.89         1.38        58.78 
TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 
       40.96        17.85         7.63         7.17        17.49         0.39 
TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 
        3.42        29.03        25.38         9.67         4.87         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 
        0.16         4.08        24.23         7.00         4.50         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 
       14.07        16.80        14.96        13.87         9.40         8.88 
TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 
       18.97         5.06        16.60         9.86        24.23        40.54 
TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 
       21.30        30.05        14.04        11.51        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 
       16.77        16.08         7.59         2.86        14.40        15.78 
TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 TCGA-32-1977 
        2.53         1.22         0.66         4.77        15.39         0.10 
TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 
       19.50         1.18         4.67        12.69        16.93        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       20.78        15.02        15.95         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       21.14        20.32         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 
        4.44        11.84         0.20        15.12        12.46         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
       20.91         4.34        14.33         7.50         4.80         4.54 
TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 
       17.59         3.09         3.65         9.17        47.93         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 
       36.85        16.70         3.29         2.70        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 
       36.20         7.63         4.73         2.83        14.73         2.50 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0126 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 
       20.38         6.94        33.67        12.95        25.35        26.70 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 
       11.90         0.20        10.29         2.20         2.33        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 
       12.33        13.94        10.45         3.19        10.82        10.65 
TCGA-06-0166 TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 
        5.85        11.41        19.66         3.29         4.47         3.22 
TCGA-06-0178 TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 
       88.14        69.90        73.84        44.58        15.42        38.96 
TCGA-06-0195 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
        7.40         0.53        15.02        24.16         0.72        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
       13.32        20.42        48.69        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 
        7.17        40.41        16.57        20.78        26.76        13.61 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
        1.08        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 
        5.95        16.64         4.37         0.43        31.50         7.79 
TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 
        5.39       120.56         7.36        18.02        14.73        12.99 
TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 
       34.92        26.66         3.65        10.62         2.24        11.24 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 
        1.35         5.39        28.93         0.79        13.78        50.53 
TCGA-16-0846 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 
        3.91        31.33        14.86         5.49         1.58         7.92 
TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        2.33         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6660 
        5.16        22.68        12.76         5.42        11.38         3.75 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

  TCF12 MUTATED TCF12 WILD-TYPE 
           5.06            0.10 
  TCF12 MUTATED TCF12 WILD-TYPE 
          22.72          120.56 
  TCF12 MUTATED TCF12 WILD-TYPE 
           7.20           11.74 
[1] "5.1 - 22.7 (7.2)"   "0.1 - 120.6 (11.7)"
[1] "hr=" "1.3"
D27V2, continuous
D27V3, binary
                 cls
clus                0   1
  TCF12 MUTATED     1   3
  TCF12 WILD-TYPE 100 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCF12 MUTATED      1    3
  TCF12 WILD-TYPE  100  176
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  FEMALE             1             100
  MALE               3             176
[1] 2 2
[1] FALSE
D27V4, binary
                 cls
clus                0   1
  TCF12 MUTATED     0   3
  TCF12 WILD-TYPE  46 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCF12 MUTATED      0    3
  TCF12 WILD-TYPE   46  214
     clus
vv    TCF12 MUTATED TCF12 WILD-TYPE
  NO              0              46
  YES             3             214
[1] 2 2
[1] FALSE
D27V5, continuous
                 vv
clus              GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  TCF12 MUTATED                               1                   0
  TCF12 WILD-TYPE                            10                   4
                 vv
clus              UNTREATED PRIMARY (DE NOVO) GBM
  TCF12 MUTATED                                 3
  TCF12 WILD-TYPE                             262
D27V6, multiclass
                                 clus
vv                                TCF12 MUTATED TCF12 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)               1              10
  TREATED PRIMARY GBM                         0               4
  UNTREATED PRIMARY (DE NOVO) GBM             3             262
[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"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TCF12 MUTATED       0                         0     4
  TCF12 WILD-TYPE     5                        17   248
D27V7, multiclass
                           clus
vv                          TCF12 MUTATED TCF12 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0              17
  WHITE                                 4             248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                 cls
clus                0   1
  TCF12 MUTATED     0   4
  TCF12 WILD-TYPE   3 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCF12 MUTATED      0    4
  TCF12 WILD-TYPE    3  218
                        clus
vv                       TCF12 MUTATED TCF12 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             4             218
[1] 2 2
[1] FALSE

Clustering(28) Variable = LZTR1 MUTATION ANALYSIS
D28V1, survival
                 sevent
clus2               0   1
  LZTR1 MUTATED     3   7
  LZTR1 WILD-TYPE  56 211
  LZTR1 MUTATED LZTR1 WILD-TYPE 
             10             267 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
              7             211 
$`LZTR1 MUTATED`
TCGA-06-5413 TCGA-06-5856 TCGA-06-6697 TCGA-14-0862 TCGA-32-1977 TCGA-32-4209 
        8.81         3.75        12.85         2.89         0.10        20.32 
TCGA-32-4210 TCGA-76-6657 TCGA-06-0188 TCGA-06-2562 
        3.72         5.03        44.58        12.56 

$`LZTR1 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5858 TCGA-06-5859 
        8.98         8.55         5.10         2.73         6.15         4.57 
TCGA-06-6388 TCGA-06-6695 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 
        5.23         8.32         4.77         1.55         4.77         4.96 
TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 
       15.35        22.19        15.22        10.95        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 
       14.93         3.22         2.04        11.97         0.95        23.05 
TCGA-14-0790 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 
       13.78         1.38        58.78        40.96        17.85         7.63 
TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 
        7.17        17.49         0.39         3.42        29.03        25.38 
TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 
        5.06         9.67         4.87         7.53         0.16         4.08 
TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 
       24.23         7.00         4.50         6.64        17.19         8.02 
TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 
       18.90         4.73        12.10         1.78        14.07        16.80 
TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 
       14.96        13.87         9.40         8.88        18.97         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 
       14.04        11.51        24.76        18.08        16.77        16.08 
TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 
        7.59         2.86        14.40        15.78         2.53         1.22 
TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        0.66         4.77        15.39        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       12.69        16.93        12.23        20.78        15.02        15.95 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4211 TCGA-32-4213 
        8.84        22.78        25.18        21.14        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 
        3.45        20.91         4.34        14.33         7.50         4.80 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 
        4.54        17.59         3.09         3.65         9.17        47.93 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        2.53        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
        8.35        20.98         4.83        23.90        34.45        18.64 
TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 
       36.20         7.63         4.73         2.83        14.73         2.50 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
       20.38         6.94        22.72        33.67        12.95        25.35 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 
       26.70        11.90         0.20        10.29         2.20         2.33 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 
       10.65         5.85        11.41        19.66         3.29         4.47 
TCGA-06-0174 TCGA-06-0178 TCGA-06-0184 TCGA-06-0185 TCGA-06-0189 TCGA-06-0192 
        3.22        88.14        69.90        73.84        15.42        38.96 
TCGA-06-0195 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
        7.40         0.53        15.02        24.16         0.72        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
       13.32        20.42        48.69        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 
        7.17        40.41        16.57        20.78        26.76        13.61 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2563 TCGA-06-2564 
        1.08        12.49         4.93        17.65        30.64         5.95 
TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 
       16.64         4.37         0.43        31.50         7.79         5.39 
TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
      120.56         7.36        18.02        14.73        12.99        34.92 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 
       26.66         3.65        10.62         2.24        11.24         1.35 
TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-16-0846 
        5.39        28.93         0.79        13.78        50.53         3.91 
TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
       31.33        14.86         5.49         1.58         7.92         2.33 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        23.44        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 
       22.68        12.76         5.42        11.38         5.42         3.75 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

  LZTR1 MUTATED LZTR1 WILD-TYPE 
           0.10            0.16 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
          44.58          120.56 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
           6.92           11.74 
[1] "0.1 - 44.6 (6.9)"   "0.2 - 120.6 (11.7)"
[1] "hr=" "1.2"
D28V2, continuous
D28V3, binary
                 cls
clus                0   1
  LZTR1 MUTATED     1   9
  LZTR1 WILD-TYPE 100 170
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED      1    9
  LZTR1 WILD-TYPE  100  170
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  FEMALE             1             100
  MALE               9             170
[1] 2 2
[1] FALSE
D28V4, binary
                 cls
clus                0   1
  LZTR1 MUTATED     3   5
  LZTR1 WILD-TYPE  43 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED      3    5
  LZTR1 WILD-TYPE   43  212
     clus
vv    LZTR1 MUTATED LZTR1 WILD-TYPE
  NO              3              43
  YES             5             212
[1] 2 2
[1] FALSE
D28V5, continuous
                 vv
clus              GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  LZTR1 MUTATED                               0                   1
  LZTR1 WILD-TYPE                            11                   3
                 vv
clus              UNTREATED PRIMARY (DE NOVO) GBM
  LZTR1 MUTATED                                 9
  LZTR1 WILD-TYPE                             256
D28V6, multiclass
                                 clus
vv                                LZTR1 MUTATED LZTR1 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)               0              11
  TREATED PRIMARY GBM                         1               3
  UNTREATED PRIMARY (DE NOVO) GBM             9             256
[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"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LZTR1 MUTATED       0                         0    10
  LZTR1 WILD-TYPE     5                        17   242
D28V7, multiclass
                           clus
vv                          LZTR1 MUTATED LZTR1 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0              17
  WHITE                                10             242
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, binary
                 cls
clus                0   1
  LZTR1 MUTATED     2   7
  LZTR1 WILD-TYPE   1 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED      2    7
  LZTR1 WILD-TYPE    1  215
                        clus
vv                       LZTR1 MUTATED LZTR1 WILD-TYPE
  HISPANIC OR LATINO                 2               1
  NOT HISPANIC OR LATINO             7             215
[1] 2 2
[1] FALSE

Clustering(29) Variable = ZDHHC4 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2                0   1
  ZDHHC4 MUTATED     0   3
  ZDHHC4 WILD-TYPE  59 215
  ZDHHC4 MUTATED ZDHHC4 WILD-TYPE 
               3              274 
  ZDHHC4 MUTATED ZDHHC4 WILD-TYPE 
               3              215 
$`ZDHHC4 MUTATED`
TCGA-41-5651 TCGA-76-6286 TCGA-76-6283 
       15.12        20.98         5.42 

$`ZDHHC4 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 
        1.55         4.77         4.96        15.35        22.19        15.22 
TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 
       11.97         0.95        23.05        13.78         2.89         1.38 
TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 
       58.78        40.96        17.85         7.63         7.17        17.49 
TCGA-14-3476 TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 
        0.39         3.42        29.03        25.38         5.06         9.67 
TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        4.87         7.53         0.16         4.08        24.23         7.00 
TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        4.50         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 
       12.10         1.78        14.07        16.80        14.96        13.87 
TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        9.40         8.88        18.97         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        18.08        16.77        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 
       14.40        15.78         2.53         1.22         0.66         4.77 
TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
       15.39         0.10        19.50         1.18         4.67        12.69 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 
       16.93        12.23        20.78        15.02        15.95         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 
       22.78        25.18        21.14        20.32         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 
       19.86        10.85        19.23         0.85        13.35         8.94 
TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 
        9.53         0.99         4.44        11.84         0.20        12.46 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 
        3.45        20.91         4.34        14.33         7.50         4.80 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 
        4.54        17.59         3.09         3.65         9.17        47.93 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        2.53        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
        8.35         4.83         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 
       36.20         7.63         4.73         2.83        14.73         2.50 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
       20.38         6.94        22.72        33.67        12.95        25.35 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 
       26.70        11.90         0.20        10.29         2.20         2.33 
TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 
       46.59        12.33        13.94        10.45         3.19        10.82 
TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 
       10.65         5.85        11.41        19.66         3.29         4.47 
TCGA-06-0174 TCGA-06-0178 TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 
        3.22        88.14        69.90        73.84        44.58        15.42 
TCGA-06-0192 TCGA-06-0195 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
       38.96         7.40         0.53        15.02        24.16         0.72 
TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 
       13.64        13.32        20.42        48.69        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       46.19         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       13.61         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
       30.64         5.95        16.64         4.37         0.43        31.50 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 
        7.79         5.39       120.56         7.36        18.02        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 
       12.99        34.92        26.66         3.65        10.62         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 
       11.24         1.35         5.39        28.93         0.79        13.78 
TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 
       50.53         3.91        31.33        14.86         5.49         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        7.92         2.33         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 
       13.64         5.16        22.68        12.76         5.42        11.38 
TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        3.75         1.61        17.72        26.30 

  ZDHHC4 MUTATED ZDHHC4 WILD-TYPE 
            5.42             0.10 
  ZDHHC4 MUTATED ZDHHC4 WILD-TYPE 
           20.98           120.56 
  ZDHHC4 MUTATED ZDHHC4 WILD-TYPE 
           15.12            11.46 
[1] "5.4 - 21.0 (15.1)"  "0.1 - 120.6 (11.5)"
[1] "hr=" "1.2"
D29V2, continuous
D29V3, binary
                  cls
clus                 0   1
  ZDHHC4 MUTATED     2   1
  ZDHHC4 WILD-TYPE  99 178
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC4 MUTATED      2    1
  ZDHHC4 WILD-TYPE   99  178
        clus
vv       ZDHHC4 MUTATED ZDHHC4 WILD-TYPE
  FEMALE              2               99
  MALE                1              178
[1] 2 2
[1] FALSE
D29V4, binary
                  cls
clus                 0   1
  ZDHHC4 MUTATED     0   2
  ZDHHC4 WILD-TYPE  46 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC4 MUTATED      0    2
  ZDHHC4 WILD-TYPE   46  215
     clus
vv    ZDHHC4 MUTATED ZDHHC4 WILD-TYPE
  NO               0               46
  YES              2              215
[1] 2 2
[1] FALSE
D29V5, continuous
[1] "Remove cluster labels:" "ZDHHC4 MUTATED"        
clus
  ZDHHC4 MUTATED ZDHHC4 WILD-TYPE 
               2              204 
      TCGA-06-1806       TCGA-06-5408       TCGA-06-5410       TCGA-06-5411 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5412       TCGA-06-5413       TCGA-06-5414       TCGA-06-5415 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5417       TCGA-06-5418       TCGA-06-5858       TCGA-06-5859 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-6388       TCGA-06-6695       TCGA-06-6697       TCGA-06-6700 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-0615       TCGA-12-1597       TCGA-12-3649       TCGA-12-3650 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-3652       TCGA-12-3653       TCGA-12-5299       TCGA-12-5301 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-14-0740       TCGA-14-0786       TCGA-14-0790       TCGA-14-0862 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-14-1395       TCGA-14-1450       TCGA-14-1456       TCGA-14-1823 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-14-1825       TCGA-14-1829       TCGA-14-2554       TCGA-14-4157 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-1390       TCGA-19-1790       TCGA-19-2619       TCGA-19-2620 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-2623       TCGA-19-2631       TCGA-19-4068       TCGA-19-5947 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-5950       TCGA-19-5951       TCGA-19-5952       TCGA-19-5954 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-5958       TCGA-19-5959       TCGA-19-5960       TCGA-26-5132 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-1830       TCGA-27-1831       TCGA-27-1832       TCGA-27-1833 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-1834       TCGA-27-1835       TCGA-27-1836       TCGA-27-1837 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-1838       TCGA-27-2518       TCGA-27-2519       TCGA-27-2521 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-2523       TCGA-27-2524       TCGA-27-2526       TCGA-27-2527 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-2528       TCGA-28-2502       TCGA-28-2509       TCGA-32-1982 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-1986       TCGA-32-2615       TCGA-32-2638       TCGA-32-4213 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-41-2571       TCGA-41-2573       TCGA-41-2575       TCGA-74-6573 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-74-6575       TCGA-74-6577       TCGA-74-6578       TCGA-74-6584 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-4925       TCGA-76-4926       TCGA-76-4927       TCGA-76-4928 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-4929       TCGA-76-4931       TCGA-76-4932       TCGA-76-4934 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-4935       TCGA-76-6191       TCGA-76-6192       TCGA-76-6193 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-6282       TCGA-76-6285       TCGA-76-6656       TCGA-76-6657 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-6661       TCGA-76-6662       TCGA-76-6663       TCGA-76-6664 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-02-0003       TCGA-02-0033       TCGA-02-0047       TCGA-02-0055 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-02-2470       TCGA-02-2483       TCGA-02-2485       TCGA-02-2486 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0126       TCGA-06-0128       TCGA-06-0129       TCGA-06-0130 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0139       TCGA-06-0140       TCGA-06-0141       TCGA-06-0151 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0154       TCGA-06-0155       TCGA-06-0157       TCGA-06-0158 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0165       TCGA-06-0167       TCGA-06-0168       TCGA-06-0169 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0174       TCGA-06-0178       TCGA-06-0184       TCGA-06-0185 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0188       TCGA-06-0192       TCGA-06-0195       TCGA-06-0214 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0216       TCGA-06-0238       TCGA-06-0240       TCGA-06-0241 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0644       TCGA-06-0646       TCGA-06-0648       TCGA-06-0686 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0743       TCGA-06-0744       TCGA-06-0745       TCGA-06-0747 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0750       TCGA-06-0875       TCGA-06-0876       TCGA-06-0878 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0879       TCGA-06-0881       TCGA-06-0882       TCGA-06-0939 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2557       TCGA-06-2558       TCGA-06-2559       TCGA-06-2561 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2562       TCGA-06-2563       TCGA-06-2564       TCGA-06-2565 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2567       TCGA-06-2569       TCGA-06-2570       TCGA-06-6389 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-6390       TCGA-08-0386       TCGA-12-0616       TCGA-12-0618 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-0619       TCGA-12-0688       TCGA-12-0692       TCGA-12-0821 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-14-0787       TCGA-14-0789       TCGA-14-0813       TCGA-14-0817 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-14-0871       TCGA-14-1043       TCGA-15-0742       TCGA-26-1442 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-26-5133       TCGA-26-5134       TCGA-26-5139       TCGA-26-6173 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-26-6174       TCGA-28-2513       TCGA-28-2514       TCGA-28-5204 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-5207       TCGA-28-5208       TCGA-28-5211       TCGA-28-5213 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-5214       TCGA-28-5215       TCGA-28-5216       TCGA-28-5219 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-5220       TCGA-76-6280       TCGA-76-6660       TCGA-81-5910 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
                  vv
clus               GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  ZDHHC4 MUTATED                               1                   0
  ZDHHC4 WILD-TYPE                            10                   4
                  vv
clus               UNTREATED PRIMARY (DE NOVO) GBM
  ZDHHC4 MUTATED                                 2
  ZDHHC4 WILD-TYPE                             263
D29V6, multiclass
                                 clus
vv                                ZDHHC4 MUTATED ZDHHC4 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                1               10
  TREATED PRIMARY GBM                          0                4
  UNTREATED PRIMARY (DE NOVO) GBM              2              263
[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"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZDHHC4 MUTATED       0                         1     2
  ZDHHC4 WILD-TYPE     5                        16   250
D29V7, multiclass
                           clus
vv                          ZDHHC4 MUTATED ZDHHC4 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              1               16
  WHITE                                  2              250
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, binary
                  cls
clus                 0   1
  ZDHHC4 MUTATED     0   3
  ZDHHC4 WILD-TYPE   3 219
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC4 MUTATED      0    3
  ZDHHC4 WILD-TYPE    3  219
                        clus
vv                       ZDHHC4 MUTATED ZDHHC4 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              3              219
[1] 2 2
[1] FALSE

Clustering(30) Variable = IL18RAP MUTATION ANALYSIS
D30V1, survival
                   sevent
clus2                 0   1
  IL18RAP MUTATED     1   5
  IL18RAP WILD-TYPE  58 213
  IL18RAP MUTATED IL18RAP WILD-TYPE 
                6               271 
  IL18RAP MUTATED IL18RAP WILD-TYPE 
                5               213 
$`IL18RAP MUTATED`
TCGA-06-6701 TCGA-14-0790 TCGA-19-5959 TCGA-32-5222 TCGA-41-5651 TCGA-06-2559 
        4.96        13.78        16.80        19.23        15.12         4.93 

$`IL18RAP WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 
        1.55         4.77        15.35        22.19        15.22        10.95 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 
       34.92        14.53        14.93         3.22         2.04        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 
        0.95        23.05         2.89         1.38        58.78        40.96 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 
       17.85         7.63         7.17        17.49         0.39         3.42 
TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 
       29.03        25.38         5.06         9.67         4.87         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 
        0.16         4.08        24.23         7.00         4.50         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 
       17.19         8.02        18.90         4.73        12.10         1.78 
TCGA-19-5958 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 
       14.07        14.96        13.87         9.40         8.88        18.97 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 
        5.06        16.60         9.86        24.23        40.54        21.30 
TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 
       30.05        14.04        11.51        24.76        18.08        16.77 
TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 
       16.08         7.59         2.86        14.40        15.78         2.53 
TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 
        1.22         0.66         4.77        15.39         0.10        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 
        1.18         4.67        12.69        16.93        12.23        20.78 
TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 
       15.02        15.95         8.84        22.78        25.18        21.14 
TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 TCGA-41-2571 
       20.32         3.72        12.59        19.86        10.85         0.85 
TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 
       13.35         8.94         9.53         0.99         4.44        11.84 
TCGA-41-4097 TCGA-41-6646 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        0.20        12.46         3.45        20.91         4.34        14.33 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 
        7.50         4.80         4.54        17.59         3.09         3.65 
TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 
        9.17        47.93         2.53        36.85        16.70         3.29 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 
        2.70        17.06         8.35        20.98         4.83         5.03 
TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 
       23.90        34.45        18.64        36.20         7.63         4.73 
TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 
        2.83        14.73         2.50        12.92        15.32        15.45 
TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 
       20.32         2.70         6.15        20.38         6.94        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 
       33.67        12.95        25.35        26.70        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.29         2.20         2.33        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 
       10.45         3.19        10.82        10.65         5.85        11.41 
TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 TCGA-06-0184 
       19.66         3.29         4.47         3.22        88.14        69.90 
TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0213 
       73.84        44.58        15.42        38.96         7.40         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       15.02        24.16         0.72        13.64        13.32        20.42 
TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 
       48.69        12.62         5.75         5.75         9.80         2.10 
TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
       23.57        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 
        2.70         0.92        43.46        46.19         7.17        40.41 
TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 
       16.57        20.78        26.76        13.61         1.08        12.49 
TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 
       17.65        12.56        30.64         5.95        16.64         4.37 
TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 
        0.43        31.50         7.79         5.39       120.56         7.36 
TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 
       18.02        14.73        12.99        34.92        26.66         3.65 
TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 
       10.62         2.24        11.24         1.35         5.39        28.93 
TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 TCGA-26-5133 
        0.79        13.78        50.53         3.91        31.33        14.86 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 
        5.49         1.58         7.92         2.33         7.30         5.26 
TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 
       14.93        11.28        17.88        14.53        11.77        31.27 
TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 
       23.44        11.01        13.64         5.16        22.68        12.76 
TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 
        5.42        11.38         5.42         3.75         1.61        17.72 
TCGA-87-5896 
       26.30 

  IL18RAP MUTATED IL18RAP WILD-TYPE 
             4.93              0.10 
  IL18RAP MUTATED IL18RAP WILD-TYPE 
            19.23            120.56 
  IL18RAP MUTATED IL18RAP WILD-TYPE 
            14.45             11.41 
[1] "4.9 - 19.2 (14.4)"  "0.1 - 120.6 (11.4)"
[1] "hr=" "1.2"
D30V2, continuous
D30V3, binary
                   cls
clus                  0   1
  IL18RAP MUTATED     3   3
  IL18RAP WILD-TYPE  98 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL18RAP MUTATED      3    3
  IL18RAP WILD-TYPE   98  176
        clus
vv       IL18RAP MUTATED IL18RAP WILD-TYPE
  FEMALE               3                98
  MALE                 3               176
[1] 2 2
[1] FALSE
D30V4, binary
                   cls
clus                  0   1
  IL18RAP MUTATED     0   6
  IL18RAP WILD-TYPE  46 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL18RAP MUTATED      0    6
  IL18RAP WILD-TYPE   46  211
     clus
vv    IL18RAP MUTATED IL18RAP WILD-TYPE
  NO                0                46
  YES               6               211
[1] 2 2
[1] FALSE
D30V5, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  IL18RAP MUTATED                               0                   0
  IL18RAP WILD-TYPE                            11                   4
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  IL18RAP MUTATED                                 6
  IL18RAP WILD-TYPE                             259
D30V6, multiclass
                                 clus
vv                                IL18RAP MUTATED IL18RAP WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                11
  TREATED PRIMARY GBM                           0                 4
  UNTREATED PRIMARY (DE NOVO) GBM               6               259
[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"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IL18RAP MUTATED       0                         1     5
  IL18RAP WILD-TYPE     5                        16   247
D30V7, multiclass
                           clus
vv                          IL18RAP MUTATED IL18RAP WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               1                16
  WHITE                                   5               247
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, binary
                   cls
clus                  0   1
  IL18RAP MUTATED     0   5
  IL18RAP WILD-TYPE   3 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL18RAP MUTATED      0    5
  IL18RAP WILD-TYPE    3  217
                        clus
vv                       IL18RAP MUTATED IL18RAP WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               5               217
[1] 2 2
[1] FALSE

Clustering(31) Variable = ODF4 MUTATION ANALYSIS
D31V1, survival
                sevent
clus2              0   1
  ODF4 MUTATED     0   3
  ODF4 WILD-TYPE  59 215
  ODF4 MUTATED ODF4 WILD-TYPE 
             3            274 
  ODF4 MUTATED ODF4 WILD-TYPE 
             3            215 
$`ODF4 MUTATED`
TCGA-19-5952 TCGA-06-0645 TCGA-06-2559 
       18.90         5.75         4.93 

$`ODF4 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 
        1.55         4.77         4.96        15.35        22.19        15.22 
TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 
       11.97         0.95        23.05        13.78         2.89         1.38 
TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 
       58.78        40.96        17.85         7.63         7.17        17.49 
TCGA-14-3476 TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 
        0.39         3.42        29.03        25.38         5.06         9.67 
TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        4.87         7.53         0.16         4.08        24.23         7.00 
TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 TCGA-19-5954 
        4.50         6.64        17.19         8.02         4.73        12.10 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 
        1.78        14.07        16.80        14.96        13.87         9.40 
TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        8.88        18.97         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       18.08        16.77        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 
       15.78         2.53         1.22         0.66         4.77        15.39 
TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 
        0.10        19.50         1.18         4.67        12.69        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 
       12.23        20.78        15.02        15.95         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       25.18        21.14        20.32         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 
        3.45        20.91         4.34        14.33         7.50         4.80 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 
        4.54        17.59         3.09         3.65         9.17        47.93 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        2.53        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 
       18.64        36.20         7.63         4.73         2.83        14.73 
TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
        2.50        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
        6.15        20.38         6.94        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       25.35        26.70        11.90         0.20        10.29         2.20 
TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
        2.33        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 
       10.82        10.65         5.85        11.41        19.66         3.29 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 
        4.47         3.22        88.14        69.90        73.84        44.58 
TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
       15.42        38.96         7.40         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 
        0.72        13.64        13.32        20.42        48.69        12.62 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       46.19         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
       13.61         1.08        12.49        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 
        5.95        16.64         4.37         0.43        31.50         7.79 
TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 
        5.39       120.56         7.36        18.02        14.73        12.99 
TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 
       34.92        26.66         3.65        10.62         2.24        11.24 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 
        1.35         5.39        28.93         0.79        13.78        50.53 
TCGA-16-0846 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 
        3.91        31.33        14.86         5.49         1.58         7.92 
TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        2.33         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 
        5.16        22.68        12.76         5.42        11.38         5.42 
TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        3.75         1.61        17.72        26.30 

  ODF4 MUTATED ODF4 WILD-TYPE 
          4.93           0.10 
  ODF4 MUTATED ODF4 WILD-TYPE 
         18.90         120.56 
  ODF4 MUTATED ODF4 WILD-TYPE 
         5.750         11.625 
[1] "4.9 - 18.9 (5.8)"   "0.1 - 120.6 (11.6)"
[1] "hr=" "1.7"
D31V2, continuous
D31V3, binary
                cls
clus               0   1
  ODF4 MUTATED     1   2
  ODF4 WILD-TYPE 100 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODF4 MUTATED      1    2
  ODF4 WILD-TYPE  100  177
        clus
vv       ODF4 MUTATED ODF4 WILD-TYPE
  FEMALE            1            100
  MALE              2            177
[1] 2 2
[1] FALSE
D31V4, binary
                cls
clus               0   1
  ODF4 MUTATED     1   2
  ODF4 WILD-TYPE  45 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODF4 MUTATED      1    2
  ODF4 WILD-TYPE   45  215
     clus
vv    ODF4 MUTATED ODF4 WILD-TYPE
  NO             1             45
  YES            2            215
[1] 2 2
[1] FALSE
D31V5, continuous
[1] "Remove cluster labels:" "ODF4 MUTATED"          
clus
  ODF4 MUTATED ODF4 WILD-TYPE 
             2            204 
    TCGA-06-1806     TCGA-06-5408     TCGA-06-5410     TCGA-06-5411 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-5412     TCGA-06-5413     TCGA-06-5414     TCGA-06-5415 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-5417     TCGA-06-5418     TCGA-06-5858     TCGA-06-5859 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-6388     TCGA-06-6695     TCGA-06-6697     TCGA-06-6700 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-12-0615     TCGA-12-1597     TCGA-12-3649     TCGA-12-3650 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-12-3652     TCGA-12-3653     TCGA-12-5299     TCGA-12-5301 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-14-0740     TCGA-14-0786     TCGA-14-0790     TCGA-14-0862 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-14-1395     TCGA-14-1450     TCGA-14-1456     TCGA-14-1823 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-14-1825     TCGA-14-1829     TCGA-14-2554     TCGA-14-4157 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-19-1390     TCGA-19-1790     TCGA-19-2619     TCGA-19-2620 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-19-2623     TCGA-19-2631     TCGA-19-4068     TCGA-19-5947 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-19-5950     TCGA-19-5951     TCGA-19-5954     TCGA-19-5958 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-19-5959     TCGA-19-5960     TCGA-26-5132     TCGA-27-1830 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-27-1831     TCGA-27-1832     TCGA-27-1833     TCGA-27-1834 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-27-1835     TCGA-27-1836     TCGA-27-1837     TCGA-27-1838 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-27-2518     TCGA-27-2519     TCGA-27-2521     TCGA-27-2523 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-27-2524     TCGA-27-2526     TCGA-27-2527     TCGA-27-2528 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-28-2502     TCGA-28-2509     TCGA-32-1982     TCGA-32-1986 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-32-2615     TCGA-32-2638     TCGA-32-4213     TCGA-41-2571 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-41-2573     TCGA-41-2575     TCGA-74-6573     TCGA-74-6575 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-74-6577     TCGA-74-6578     TCGA-74-6584     TCGA-76-4925 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-76-4926     TCGA-76-4927     TCGA-76-4928     TCGA-76-4929 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-76-4931     TCGA-76-4932     TCGA-76-4934     TCGA-76-4935 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-76-6191     TCGA-76-6192     TCGA-76-6193     TCGA-76-6282 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-76-6285     TCGA-76-6286     TCGA-76-6656     TCGA-76-6657 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-76-6661     TCGA-76-6662     TCGA-76-6663     TCGA-76-6664 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-02-0003     TCGA-02-0033     TCGA-02-0047     TCGA-02-0055 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-02-2470     TCGA-02-2483     TCGA-02-2485     TCGA-02-2486 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-0126     TCGA-06-0128     TCGA-06-0129     TCGA-06-0130 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-0139     TCGA-06-0140     TCGA-06-0141     TCGA-06-0151 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-0154     TCGA-06-0155     TCGA-06-0157     TCGA-06-0158 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-0165     TCGA-06-0167     TCGA-06-0168     TCGA-06-0169 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-0174     TCGA-06-0178     TCGA-06-0184     TCGA-06-0185 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-0188     TCGA-06-0192     TCGA-06-0195     TCGA-06-0214 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-0216     TCGA-06-0238     TCGA-06-0240     TCGA-06-0241 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-0644     TCGA-06-0646     TCGA-06-0648     TCGA-06-0686 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-0743     TCGA-06-0744     TCGA-06-0745     TCGA-06-0747 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-0750     TCGA-06-0875     TCGA-06-0876     TCGA-06-0878 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-0879     TCGA-06-0881     TCGA-06-0882     TCGA-06-0939 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-2557     TCGA-06-2558     TCGA-06-2561     TCGA-06-2562 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-2563     TCGA-06-2564     TCGA-06-2565     TCGA-06-2567 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-06-2569     TCGA-06-2570     TCGA-06-6389     TCGA-06-6390 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-08-0386     TCGA-12-0616     TCGA-12-0618     TCGA-12-0619 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-12-0688     TCGA-12-0692     TCGA-12-0821     TCGA-14-0787 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-14-0789     TCGA-14-0813     TCGA-14-0817     TCGA-14-0871 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-14-1043     TCGA-15-0742     TCGA-26-1442     TCGA-26-5133 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-26-5134     TCGA-26-5139     TCGA-26-6173     TCGA-26-6174 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-28-2513     TCGA-28-2514     TCGA-28-5204     TCGA-28-5207 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-28-5208     TCGA-28-5211     TCGA-28-5213     TCGA-28-5214 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-28-5215     TCGA-28-5216     TCGA-28-5219     TCGA-28-5220 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
    TCGA-76-6280     TCGA-76-6283     TCGA-76-6660     TCGA-81-5910 
"ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" "ODF4 WILD-TYPE" 
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  ODF4 MUTATED                               0                   0
  ODF4 WILD-TYPE                            11                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  ODF4 MUTATED                                 3
  ODF4 WILD-TYPE                             262
D31V6, multiclass
                                 clus
vv                                ODF4 MUTATED ODF4 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              0             11
  TREATED PRIMARY GBM                        0              4
  UNTREATED PRIMARY (DE NOVO) GBM            3            262
[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"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ODF4 MUTATED       0                         0     3
  ODF4 WILD-TYPE     5                        17   249
D31V7, multiclass
                           clus
vv                          ODF4 MUTATED ODF4 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0             17
  WHITE                                3            249
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                cls
clus               0   1
  ODF4 MUTATED     0   3
  ODF4 WILD-TYPE   3 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODF4 MUTATED      0    3
  ODF4 WILD-TYPE    3  219
                        clus
vv                       ODF4 MUTATED ODF4 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            3            219
[1] 2 2
[1] FALSE

Clustering(32) Variable = KEL MUTATION ANALYSIS
D32V1, survival
               sevent
clus2             0   1
  KEL MUTATED     3  12
  KEL WILD-TYPE  56 206
  KEL MUTATED KEL WILD-TYPE 
           15           262 
  KEL MUTATED KEL WILD-TYPE 
           12           206 
$`KEL MUTATED`
TCGA-06-5408 TCGA-06-5412 TCGA-06-5414 TCGA-06-5415 TCGA-12-5301 TCGA-26-5135 
       11.74         4.54         8.98         8.55         2.04         8.88 
TCGA-41-2572 TCGA-76-4929 TCGA-06-0145 TCGA-06-0152 TCGA-06-0192 TCGA-06-0238 
       13.35         3.65         2.33        12.33        38.96        13.32 
TCGA-06-0879 TCGA-06-2558 TCGA-06-2563 
       40.41        12.49        30.64 

$`KEL WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5410 TCGA-06-5411 TCGA-06-5413 TCGA-06-5417 
        1.48        15.32         3.55         8.35         8.81         5.10 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 
        2.73         3.75         6.15         4.57         5.23         8.32 
TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 
       12.85         4.77         1.55         4.77         4.96        15.35 
TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       22.19        15.22        10.95        34.92        14.53        14.93 
TCGA-12-5299 TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 
        3.22        11.97         0.95        23.05        13.78         2.89 
TCGA-14-1395 TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 
        1.38        58.78        40.96        17.85         7.63         7.17 
TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 
       17.49         0.39         3.42        29.03        25.38         5.06 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 
        9.67         4.87         7.53         0.16         4.08        24.23 
TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 
        7.00         4.50         6.64        17.19         8.02        18.90 
TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 
        4.73        12.10         1.78        14.07        16.80        14.96 
TCGA-26-1439 TCGA-26-5132 TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
       13.87         9.40        18.97         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        18.08        16.77        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 
       14.40        15.78         2.53         1.22         0.66         4.77 
TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 
       15.39         0.10        19.50         1.18         4.67        12.69 
TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 
       16.93        12.23        20.78        15.02        15.95         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 
       22.78        25.18        21.14        20.32         3.72        12.59 
TCGA-32-4213 TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2573 TCGA-41-2575 
       19.86        10.85        19.23         0.85         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 
        3.45        20.91         4.34        14.33         7.50         4.80 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 
        4.54        17.59         3.09         9.17        47.93         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 
       36.85        16.70         3.29         2.70        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 
       36.20         7.63         4.73         2.83        14.73         2.50 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
       20.38         6.94        22.72        33.67        12.95        25.35 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0151 
       26.70        11.90         0.20        10.29         2.20        46.59 
TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 
       13.94        10.45         3.19        10.82        10.65         5.85 
TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 
       11.41        19.66         3.29         4.47         3.22        88.14 
TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0195 TCGA-06-0213 
       69.90        73.84        44.58        15.42         7.40         0.53 
TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0240 TCGA-06-0241 
       15.02        24.16         0.72        13.64        20.42        48.69 
TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 
       12.62         5.75         5.75         9.80         2.10        23.57 
TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 
       14.20        26.40        46.88         7.86         2.70         2.70 
TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 
        0.92        43.46        46.19         7.17        16.57        20.78 
TCGA-06-0939 TCGA-06-1804 TCGA-06-2557 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       26.76        13.61         1.08         4.93        17.65        12.56 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 
        5.95        16.64         4.37         0.43        31.50         7.79 
TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 
        5.39       120.56         7.36        18.02        14.73        12.99 
TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 
       34.92        26.66         3.65        10.62         2.24        11.24 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 
        1.35         5.39        28.93         0.79        13.78        50.53 
TCGA-16-0846 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 
        3.91        31.33        14.86         5.49         1.58         7.92 
TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        2.33         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 
        5.16        22.68        12.76         5.42        11.38         5.42 
TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        3.75         1.61        17.72        26.30 

  KEL MUTATED KEL WILD-TYPE 
         2.04          0.10 
  KEL MUTATED KEL WILD-TYPE 
        40.41        120.56 
  KEL MUTATED KEL WILD-TYPE 
        11.74         11.46 
[1] "2.0 - 40.4 (11.7)"  "0.1 - 120.6 (11.5)"
[1] "hr=" "1.1"
D32V2, continuous
D32V3, binary
               cls
clus              0   1
  KEL MUTATED     7   8
  KEL WILD-TYPE  94 171
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED      7    8
  KEL WILD-TYPE   94  171
        clus
vv       KEL MUTATED KEL WILD-TYPE
  FEMALE           7            94
  MALE             8           171
[1] 2 2
[1] FALSE
D32V4, binary
               cls
clus              0   1
  KEL MUTATED     1  12
  KEL WILD-TYPE  45 205
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED      1   12
  KEL WILD-TYPE   45  205
     clus
vv    KEL MUTATED KEL WILD-TYPE
  NO            1            45
  YES          12           205
[1] 2 2
[1] FALSE
D32V5, continuous
               vv
clus            GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  KEL MUTATED                               0                   0
  KEL WILD-TYPE                            11                   4
               vv
clus            UNTREATED PRIMARY (DE NOVO) GBM
  KEL MUTATED                                15
  KEL WILD-TYPE                             250
D32V6, multiclass
                                 clus
vv                                KEL MUTATED KEL WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)             0            11
  TREATED PRIMARY GBM                       0             4
  UNTREATED PRIMARY (DE NOVO) GBM          15           250
[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"
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KEL MUTATED       0                         0    15
  KEL WILD-TYPE     5                        17   237
D32V7, multiclass
                           clus
vv                          KEL MUTATED KEL WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0            17
  WHITE                              15           237
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
               cls
clus              0   1
  KEL MUTATED     0  15
  KEL WILD-TYPE   3 207
[1] "tbl2"
               cls
clus            [,1] [,2]
  KEL MUTATED      0   15
  KEL WILD-TYPE    3  207
                        clus
vv                       KEL MUTATED KEL WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO          15           207
[1] 2 2
[1] FALSE

Clustering(33) Variable = TESK1 MUTATION ANALYSIS
D33V1, survival
                 sevent
clus2               0   1
  TESK1 MUTATED     0   2
  TESK1 WILD-TYPE  59 216
  TESK1 MUTATED TESK1 WILD-TYPE 
              2             275 
  TESK1 MUTATED TESK1 WILD-TYPE 
              2             216 
$`TESK1 MUTATED`
TCGA-12-3649 TCGA-06-0241 
       15.22        48.69 

$`TESK1 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3650 
        1.55         4.77         4.96        15.35        22.19        10.95 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 
       34.92        14.53        14.93         3.22         2.04        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 
        0.95        23.05        13.78         2.89         1.38        58.78 
TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 
       40.96        17.85         7.63         7.17        17.49         0.39 
TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 
        3.42        29.03        25.38         5.06         9.67         4.87 
TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 
        7.53         0.16         4.08        24.23         7.00         4.50 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 
        1.78        14.07        16.80        14.96        13.87         9.40 
TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        8.88        18.97         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       18.08        16.77        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 
       15.78         2.53         1.22         0.66         4.77        15.39 
TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-1991 
        0.10        19.50         1.18         4.67        12.69        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 
       12.23        20.78        15.02        15.95         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       25.18        21.14        20.32         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 
        3.45        20.91         4.34        14.33         7.50         4.80 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 
        4.54        17.59         3.09         3.65         9.17        47.93 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        2.53        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 
       18.64        36.20         7.63         4.73         2.83        14.73 
TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 
        2.50        12.92        15.32        15.45        20.32         2.70 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 
        6.15        20.38         6.94        22.72        33.67        12.95 
TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 
       25.35        26.70        11.90         0.20        10.29         2.20 
TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 
        2.33        46.59        12.33        13.94        10.45         3.19 
TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 
       10.82        10.65         5.85        11.41        19.66         3.29 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 
        4.47         3.22        88.14        69.90        73.84        44.58 
TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
       15.42        38.96         7.40         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0644 TCGA-06-0645 
        0.72        13.64        13.32        20.42        12.62         5.75 
TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 
        5.75         9.80         2.10        23.57        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 
       46.19         7.17        40.41        16.57        20.78        26.76 
TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       13.61         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
       30.64         5.95        16.64         4.37         0.43        31.50 
TCGA-06-6389 TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 
        7.79         5.39       120.56         7.36        18.02        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 
       12.99        34.92        26.66         3.65        10.62         2.24 
TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 
       11.24         1.35         5.39        28.93         0.79        13.78 
TCGA-15-1444 TCGA-16-0846 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 
       50.53         3.91        31.33        14.86         5.49         1.58 
TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        7.92         2.33         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 
       17.88        14.53        11.77        31.27        23.44        11.01 
TCGA-28-5216 TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 
       13.64         5.16        22.68        12.76         5.42        11.38 
TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        5.42         3.75         1.61        17.72        26.30 

  TESK1 MUTATED TESK1 WILD-TYPE 
          15.22            0.10 
  TESK1 MUTATED TESK1 WILD-TYPE 
          48.69          120.56 
  TESK1 MUTATED TESK1 WILD-TYPE 
         31.955          11.410 
[1] "15.2 - 48.7 (32.0)" "0.1 - 120.6 (11.4)"
[1] "Remove cluster labels:" "TESK1 MUTATED"         
D33V2, continuous
D33V3, binary
                 cls
clus                0   1
  TESK1 MUTATED     1   2
  TESK1 WILD-TYPE 100 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TESK1 MUTATED      1    2
  TESK1 WILD-TYPE  100  177
        clus
vv       TESK1 MUTATED TESK1 WILD-TYPE
  FEMALE             1             100
  MALE               2             177
[1] 2 2
[1] FALSE
D33V4, binary
                 cls
clus                0   1
  TESK1 MUTATED     1   2
  TESK1 WILD-TYPE  45 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TESK1 MUTATED      1    2
  TESK1 WILD-TYPE   45  215
     clus
vv    TESK1 MUTATED TESK1 WILD-TYPE
  NO              1              45
  YES             2             215
[1] 2 2
[1] FALSE
D33V5, continuous
[1] "Remove cluster labels:" "TESK1 MUTATED"         
clus
  TESK1 MUTATED TESK1 WILD-TYPE 
              2             204 
     TCGA-06-1806      TCGA-06-5408      TCGA-06-5410      TCGA-06-5411 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-06-5412      TCGA-06-5413      TCGA-06-5414      TCGA-06-5415 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-06-5417      TCGA-06-5418      TCGA-06-5858      TCGA-06-5859 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-06-6388      TCGA-06-6695      TCGA-06-6697      TCGA-06-6700 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-12-0615      TCGA-12-1597      TCGA-12-3650      TCGA-12-3652 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-12-3653      TCGA-12-5299      TCGA-12-5301      TCGA-14-0740 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-14-0786      TCGA-14-0790      TCGA-14-0862      TCGA-14-1395 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-14-1450      TCGA-14-1456      TCGA-14-1823      TCGA-14-1825 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-14-1829      TCGA-14-2554      TCGA-14-4157      TCGA-19-1390 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-19-1790      TCGA-19-2619      TCGA-19-2620      TCGA-19-2623 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-19-2631      TCGA-19-4068      TCGA-19-5947      TCGA-19-5950 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-19-5951      TCGA-19-5952      TCGA-19-5954      TCGA-19-5958 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-19-5959      TCGA-19-5960      TCGA-26-5132      TCGA-27-1830 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-27-1831      TCGA-27-1832      TCGA-27-1833      TCGA-27-1834 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-27-1835      TCGA-27-1836      TCGA-27-1837      TCGA-27-1838 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-27-2518      TCGA-27-2519      TCGA-27-2521      TCGA-27-2523 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-27-2524      TCGA-27-2526      TCGA-27-2527      TCGA-27-2528 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-28-2502      TCGA-28-2509      TCGA-32-1982      TCGA-32-1986 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-32-2615      TCGA-32-2638      TCGA-32-4213      TCGA-41-2571 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-41-2573      TCGA-41-2575      TCGA-74-6573      TCGA-74-6575 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-74-6577      TCGA-74-6578      TCGA-74-6584      TCGA-76-4925 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-76-4926      TCGA-76-4927      TCGA-76-4928      TCGA-76-4929 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-76-4931      TCGA-76-4932      TCGA-76-4934      TCGA-76-4935 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-76-6191      TCGA-76-6192      TCGA-76-6193      TCGA-76-6282 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-76-6285      TCGA-76-6286      TCGA-76-6656      TCGA-76-6657 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-76-6661      TCGA-76-6662      TCGA-76-6663      TCGA-76-6664 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-02-0003      TCGA-02-0033      TCGA-02-0047      TCGA-02-0055 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-02-2470      TCGA-02-2483      TCGA-02-2485      TCGA-02-2486 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-06-0126      TCGA-06-0128      TCGA-06-0129      TCGA-06-0130 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-06-0139      TCGA-06-0140      TCGA-06-0141      TCGA-06-0151 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-06-0154      TCGA-06-0155      TCGA-06-0157      TCGA-06-0158 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-06-0165      TCGA-06-0167      TCGA-06-0168      TCGA-06-0169 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-06-0174      TCGA-06-0178      TCGA-06-0184      TCGA-06-0185 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-06-0188      TCGA-06-0192      TCGA-06-0195      TCGA-06-0214 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-06-0216      TCGA-06-0238      TCGA-06-0240      TCGA-06-0644 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-06-0646      TCGA-06-0648      TCGA-06-0686      TCGA-06-0743 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-06-0744      TCGA-06-0745      TCGA-06-0747      TCGA-06-0750 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-06-0875      TCGA-06-0876      TCGA-06-0878      TCGA-06-0879 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-06-0881      TCGA-06-0882      TCGA-06-0939      TCGA-06-2557 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-06-2558      TCGA-06-2559      TCGA-06-2561      TCGA-06-2562 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-06-2563      TCGA-06-2564      TCGA-06-2565      TCGA-06-2567 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-06-2569      TCGA-06-2570      TCGA-06-6389      TCGA-06-6390 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-08-0386      TCGA-12-0616      TCGA-12-0618      TCGA-12-0619 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-12-0688      TCGA-12-0692      TCGA-12-0821      TCGA-14-0787 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-14-0789      TCGA-14-0813      TCGA-14-0817      TCGA-14-0871 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-14-1043      TCGA-15-0742      TCGA-26-1442      TCGA-26-5133 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-26-5134      TCGA-26-5139      TCGA-26-6173      TCGA-26-6174 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-28-2513      TCGA-28-2514      TCGA-28-5204      TCGA-28-5207 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-28-5208      TCGA-28-5211      TCGA-28-5213      TCGA-28-5214 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-28-5215      TCGA-28-5216      TCGA-28-5219      TCGA-28-5220 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-76-6280      TCGA-76-6283      TCGA-76-6660      TCGA-81-5910 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
                 vv
clus              GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  TESK1 MUTATED                               0                   0
  TESK1 WILD-TYPE                            11                   4
                 vv
clus              UNTREATED PRIMARY (DE NOVO) GBM
  TESK1 MUTATED                                 3
  TESK1 WILD-TYPE                             262
D33V6, multiclass
                                 clus
vv                                TESK1 MUTATED TESK1 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)               0              11
  TREATED PRIMARY GBM                         0               4
  UNTREATED PRIMARY (DE NOVO) GBM             3             262
[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"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TESK1 MUTATED       0                         0     3
  TESK1 WILD-TYPE     5                        17   249
D33V7, multiclass
                           clus
vv                          TESK1 MUTATED TESK1 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0              17
  WHITE                                 3             249
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                 cls
clus                0   1
  TESK1 MUTATED     0   3
  TESK1 WILD-TYPE   3 219
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TESK1 MUTATED      0    3
  TESK1 WILD-TYPE    3  219
                        clus
vv                       TESK1 MUTATED TESK1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             219
[1] 2 2
[1] FALSE

Clustering(34) Variable = MUC17 MUTATION ANALYSIS
D34V1, survival
                 sevent
clus2               0   1
  MUC17 MUTATED     2  20
  MUC17 WILD-TYPE  57 198
  MUC17 MUTATED MUC17 WILD-TYPE 
             22             255 
  MUC17 MUTATED MUC17 WILD-TYPE 
             20             198 
$`MUC17 MUTATED`
TCGA-06-5418 TCGA-14-1823 TCGA-19-5953 TCGA-19-5954 TCGA-27-2523 TCGA-32-2491 
        2.73        17.85         4.73        12.10        16.08        12.23 
TCGA-32-4213 TCGA-76-6192 TCGA-76-6286 TCGA-02-0003 TCGA-06-0124 TCGA-06-0168 
       19.86         3.29        20.98         4.73        20.38        19.66 
TCGA-06-0645 TCGA-06-0650 TCGA-06-0939 TCGA-06-2557 TCGA-12-0821 TCGA-16-0846 
        5.75        23.57        26.76         1.08        10.62         3.91 
TCGA-28-5204 TCGA-28-5216 TCGA-28-5218 TCGA-76-6660 
       14.93        13.64         5.16         3.75 

$`MUC17 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5856 TCGA-06-5858 
        8.81         8.98         8.55         5.10         3.75         6.15 
TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 
        4.57         5.23         8.32        12.85         4.77         1.55 
TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 TCGA-12-3650 
        4.77         4.96        15.35        22.19        15.22        10.95 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 
       34.92        14.53        14.93         3.22         2.04        11.97 
TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 TCGA-14-1450 
        0.95        23.05        13.78         2.89         1.38        58.78 
TCGA-14-1456 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-14-3476 TCGA-14-4157 
       40.96         7.63         7.17        17.49         0.39         3.42 
TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 TCGA-19-2620 TCGA-19-2623 
       29.03        25.38         5.06         9.67         4.87         7.53 
TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 TCGA-19-4068 TCGA-19-5947 
        0.16         4.08        24.23         7.00         4.50         6.64 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 
       17.19         8.02        18.90         1.78        14.07        16.80 
TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 
       14.96        13.87         9.40         8.88        18.97         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 
       16.60         9.86        24.23        40.54        21.30        30.05 
TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2524 
       14.04        11.51        24.76        18.08        16.77         7.59 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 
        2.86        14.40        15.78         2.53         1.22         0.66 
TCGA-28-2509 TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 
        4.77        15.39         0.10        19.50         1.18         4.67 
TCGA-32-1986 TCGA-32-1991 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 
       12.69        16.93        20.78        15.02        15.95         8.84 
TCGA-32-2634 TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 
       22.78        25.18        21.14        20.32         3.72        12.59 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 
        3.45        20.91         4.34        14.33         7.50         4.80 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 
        4.54        17.59         3.09         3.65         9.17        47.93 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 
        2.53        36.85        16.70         2.70        17.06         8.35 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-06-0209 TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 TCGA-02-2483 
        7.63         2.83        14.73         2.50        12.92        15.32 
TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0126 TCGA-06-0128 
       15.45        20.32         2.70         6.15         6.94        22.72 
TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 
       33.67        12.95        25.35        26.70        11.90         0.20 
TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 
       10.29         2.20         2.33        46.59        12.33        13.94 
TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 TCGA-06-0166 TCGA-06-0167 
       10.45         3.19        10.82        10.65         5.85        11.41 
TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 TCGA-06-0184 TCGA-06-0185 
        3.29         4.47         3.22        88.14        69.90        73.84 
TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 TCGA-06-0195 TCGA-06-0213 TCGA-06-0214 
       44.58        15.42        38.96         7.40         0.53        15.02 
TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 
       24.16         0.72        13.64        13.32        20.42        48.69 
TCGA-06-0644 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0686 TCGA-06-0743 
       12.62         5.75         9.80         2.10        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-1804 
       46.19         7.17        40.41        16.57        20.78        13.61 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 
       16.64         4.37         0.43        31.50         7.79         5.39 
TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
      120.56         7.36        18.02        14.73        12.99        34.92 
TCGA-12-0688 TCGA-12-0692 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 
       26.66         3.65         2.24        11.24         1.35         5.39 
TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-26-1442 TCGA-26-5133 
       28.93         0.79        13.78        50.53        31.33        14.86 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 
        5.49         1.58         7.92         2.33         7.30         5.26 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 
       11.28        17.88        14.53        11.77        31.27        23.44 
TCGA-28-5215 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 
       11.01        22.68        12.76         5.42        11.38         5.42 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

  MUC17 MUTATED MUC17 WILD-TYPE 
           1.08            0.10 
  MUC17 MUTATED MUC17 WILD-TYPE 
          26.76          120.56 
  MUC17 MUTATED MUC17 WILD-TYPE 
         12.165          11.410 
[1] "1.1 - 26.8 (12.2)"  "0.1 - 120.6 (11.4)"
[1] "hr=" "1.3"
D34V2, continuous
D34V3, binary
                 cls
clus                0   1
  MUC17 MUTATED     8  14
  MUC17 WILD-TYPE  93 165
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED      8   14
  MUC17 WILD-TYPE   93  165
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  FEMALE             8              93
  MALE              14             165
[1] 2 2
[1] FALSE
D34V4, binary
                 cls
clus                0   1
  MUC17 MUTATED     4  16
  MUC17 WILD-TYPE  42 201
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED      4   16
  MUC17 WILD-TYPE   42  201
     clus
vv    MUC17 MUTATED MUC17 WILD-TYPE
  NO              4              42
  YES            16             201
[1] 2 2
[1] FALSE
D34V5, continuous
                 vv
clus              GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  MUC17 MUTATED                               1                   0
  MUC17 WILD-TYPE                            10                   4
                 vv
clus              UNTREATED PRIMARY (DE NOVO) GBM
  MUC17 MUTATED                                21
  MUC17 WILD-TYPE                             244
D34V6, multiclass
                                 clus
vv                                MUC17 MUTATED MUC17 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)               1              10
  TREATED PRIMARY GBM                         0               4
  UNTREATED PRIMARY (DE NOVO) GBM            21             244
[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"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC17 MUTATED       0                         1    21
  MUC17 WILD-TYPE     5                        16   231
D34V7, multiclass
                           clus
vv                          MUC17 MUTATED MUC17 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             1              16
  WHITE                                21             231
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, binary
                 cls
clus                0   1
  MUC17 MUTATED     0  18
  MUC17 WILD-TYPE   3 204
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED      0   18
  MUC17 WILD-TYPE    3  204
                        clus
vv                       MUC17 MUTATED MUC17 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            18             204
[1] 2 2
[1] FALSE

Clustering(35) Variable = FAM126B MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                 0   1
  FAM126B MUTATED     0   4
  FAM126B WILD-TYPE  59 214
  FAM126B MUTATED FAM126B WILD-TYPE 
                4               273 
  FAM126B MUTATED FAM126B WILD-TYPE 
                4               214 
$`FAM126B MUTATED`
TCGA-19-2631 TCGA-32-1991 TCGA-02-0033 TCGA-06-0879 
        7.00        16.93         2.83        40.41 

$`FAM126B WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 
        1.55         4.77         4.96        15.35        22.19        15.22 
TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 
       11.97         0.95        23.05        13.78         2.89         1.38 
TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 
       58.78        40.96        17.85         7.63         7.17        17.49 
TCGA-14-3476 TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 
        0.39         3.42        29.03        25.38         5.06         9.67 
TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-4068 
        4.87         7.53         0.16         4.08        24.23         4.50 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 TCGA-26-5132 
        1.78        14.07        16.80        14.96        13.87         9.40 
TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1833 
        8.88        18.97         5.06        16.60         9.86        24.23 
TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       40.54        21.30        30.05        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2527 
       18.08        16.77        16.08         7.59         2.86        14.40 
TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 TCGA-32-1970 
       15.78         2.53         1.22         0.66         4.77        15.39 
TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1986 TCGA-32-2491 
        0.10        19.50         1.18         4.67        12.69        12.23 
TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 
       20.78        15.02        15.95         8.84        22.78        25.18 
TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 TCGA-32-4719 
       21.14        20.32         3.72        12.59        19.86        10.85 
TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 TCGA-41-3392 
       19.23         0.85        13.35         8.94         9.53         0.99 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 TCGA-74-6573 
        4.44        11.84         0.20        15.12        12.46         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 
       20.91         4.34        14.33         7.50         4.80         4.54 
TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 
       17.59         3.09         3.65         9.17        47.93         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 
       36.85        16.70         3.29         2.70        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 TCGA-02-0047 TCGA-02-0055 TCGA-02-2470 
       36.20         7.63         4.73        14.73         2.50        12.92 
TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 TCGA-06-0124 
       15.32        15.45        20.32         2.70         6.15        20.38 
TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 TCGA-06-0137 
        6.94        22.72        33.67        12.95        25.35        26.70 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0142 TCGA-06-0145 TCGA-06-0151 
       11.90         0.20        10.29         2.20         2.33        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 
       12.33        13.94        10.45         3.19        10.82        10.65 
TCGA-06-0166 TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 
        5.85        11.41        19.66         3.29         4.47         3.22 
TCGA-06-0178 TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 
       88.14        69.90        73.84        44.58        15.42        38.96 
TCGA-06-0195 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
        7.40         0.53        15.02        24.16         0.72        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
       13.32        20.42        48.69        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0878 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 TCGA-06-2557 
        7.17        16.57        20.78        26.76        13.61         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 TCGA-06-6390 
       16.64         4.37         0.43        31.50         7.79         5.39 
TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 
      120.56         7.36        18.02        14.73        12.99        34.92 
TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 
       26.66         3.65        10.62         2.24        11.24         1.35 
TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 TCGA-16-0846 
        5.39        28.93         0.79        13.78        50.53         3.91 
TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 
       31.33        14.86         5.49         1.58         7.92         2.33 
TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 
        7.30         5.26        14.93        11.28        17.88        14.53 
TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.77        31.27        23.44        11.01        13.64         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 TCGA-76-6660 
       22.68        12.76         5.42        11.38         5.42         3.75 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

  FAM126B MUTATED FAM126B WILD-TYPE 
             2.83              0.10 
  FAM126B MUTATED FAM126B WILD-TYPE 
            40.41            120.56 
  FAM126B MUTATED FAM126B WILD-TYPE 
           11.965            11.510 
[1] "2.8 - 40.4 (12.0)"  "0.1 - 120.6 (11.5)"
[1] "hr=" "1.1"
D35V2, continuous
D35V3, binary
                   cls
clus                  0   1
  FAM126B MUTATED     1   3
  FAM126B WILD-TYPE 100 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM126B MUTATED      1    3
  FAM126B WILD-TYPE  100  176
        clus
vv       FAM126B MUTATED FAM126B WILD-TYPE
  FEMALE               1               100
  MALE                 3               176
[1] 2 2
[1] FALSE
D35V4, binary
                   cls
clus                  0   1
  FAM126B MUTATED     0   4
  FAM126B WILD-TYPE  46 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM126B MUTATED      0    4
  FAM126B WILD-TYPE   46  213
     clus
vv    FAM126B MUTATED FAM126B WILD-TYPE
  NO                0                46
  YES               4               213
[1] 2 2
[1] FALSE
D35V5, continuous
                   vv
clus                GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  FAM126B MUTATED                               0                   0
  FAM126B WILD-TYPE                            11                   4
                   vv
clus                UNTREATED PRIMARY (DE NOVO) GBM
  FAM126B MUTATED                                 4
  FAM126B WILD-TYPE                             261
D35V6, multiclass
                                 clus
vv                                FAM126B MUTATED FAM126B WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)                 0                11
  TREATED PRIMARY GBM                           0                 4
  UNTREATED PRIMARY (DE NOVO) GBM               4               261
[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"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM126B MUTATED       0                         0     4
  FAM126B WILD-TYPE     5                        17   248
D35V7, multiclass
                           clus
vv                          FAM126B MUTATED FAM126B WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                17
  WHITE                                   4               248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                   cls
clus                  0   1
  FAM126B MUTATED     0   3
  FAM126B WILD-TYPE   3 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM126B MUTATED      0    3
  FAM126B WILD-TYPE    3  219
                        clus
vv                       FAM126B MUTATED FAM126B WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               3               219
[1] 2 2
[1] FALSE

Clustering(36) Variable = DDX5 MUTATION ANALYSIS
D36V1, survival
                sevent
clus2              0   1
  DDX5 MUTATED     0   4
  DDX5 WILD-TYPE  59 214
  DDX5 MUTATED DDX5 WILD-TYPE 
             4            273 
  DDX5 MUTATED DDX5 WILD-TYPE 
             4            214 
$`DDX5 MUTATED`
TCGA-32-1986 TCGA-76-4925 TCGA-06-0142 TCGA-76-6660 
       12.69         4.80         2.20         3.75 

$`DDX5 WILD-TYPE`
TCGA-06-6391 TCGA-06-1806 TCGA-06-5408 TCGA-06-5410 TCGA-06-5411 TCGA-06-5412 
        1.48        15.32        11.74         3.55         8.35         4.54 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5418 TCGA-06-5856 
        8.81         8.98         8.55         5.10         2.73         3.75 
TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
        6.15         4.57         5.23         8.32        12.85         4.77 
TCGA-06-6699 TCGA-06-6700 TCGA-06-6701 TCGA-12-0615 TCGA-12-1597 TCGA-12-3649 
        1.55         4.77         4.96        15.35        22.19        15.22 
TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 
       10.95        34.92        14.53        14.93         3.22         2.04 
TCGA-14-0740 TCGA-14-0781 TCGA-14-0786 TCGA-14-0790 TCGA-14-0862 TCGA-14-1395 
       11.97         0.95        23.05        13.78         2.89         1.38 
TCGA-14-1450 TCGA-14-1456 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 
       58.78        40.96        17.85         7.63         7.17        17.49 
TCGA-14-3476 TCGA-14-4157 TCGA-16-1045 TCGA-19-1390 TCGA-19-1790 TCGA-19-2619 
        0.39         3.42        29.03        25.38         5.06         9.67 
TCGA-19-2620 TCGA-19-2623 TCGA-19-2624 TCGA-19-2625 TCGA-19-2629 TCGA-19-2631 
        4.87         7.53         0.16         4.08        24.23         7.00 
TCGA-19-4068 TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 
        4.50         6.64        17.19         8.02        18.90         4.73 
TCGA-19-5954 TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-26-1439 
       12.10         1.78        14.07        16.80        14.96        13.87 
TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        9.40         8.88        18.97         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1836 TCGA-27-1837 TCGA-27-1838 
       24.23        40.54        21.30        30.05        14.04        11.51 
TCGA-27-2518 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 
       24.76        18.08        16.77        16.08         7.59         2.86 
TCGA-27-2527 TCGA-27-2528 TCGA-28-1747 TCGA-28-1753 TCGA-28-2502 TCGA-28-2509 
       14.40        15.78         2.53         1.22         0.66         4.77 
TCGA-32-1970 TCGA-32-1977 TCGA-32-1979 TCGA-32-1980 TCGA-32-1982 TCGA-32-1991 
       15.39         0.10        19.50         1.18         4.67        16.93 
TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 TCGA-32-2632 TCGA-32-2634 
       12.23        20.78        15.02        15.95         8.84        22.78 
TCGA-32-2638 TCGA-32-4208 TCGA-32-4209 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
       25.18        21.14        20.32         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-41-6646 
        0.99         4.44        11.84         0.20        15.12        12.46 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4926 
        3.45        20.91         4.34        14.33         7.50         4.54 
TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-76-4934 
       17.59         3.09         3.65         9.17        47.93         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 TCGA-76-6285 
       36.85        16.70         3.29         2.70        17.06         8.35 
TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 
       20.98         4.83         5.03        23.90        34.45        18.64 
TCGA-76-6664 TCGA-06-0209 TCGA-02-0003 TCGA-02-0033 TCGA-02-0047 TCGA-02-0055 
       36.20         7.63         4.73         2.83        14.73         2.50 
TCGA-02-2470 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0119 TCGA-06-0122 
       12.92        15.32        15.45        20.32         2.70         6.15 
TCGA-06-0124 TCGA-06-0126 TCGA-06-0128 TCGA-06-0129 TCGA-06-0130 TCGA-06-0132 
       20.38         6.94        22.72        33.67        12.95        25.35 
TCGA-06-0137 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0145 TCGA-06-0151 
       26.70        11.90         0.20        10.29         2.33        46.59 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0157 TCGA-06-0158 TCGA-06-0165 
       12.33        13.94        10.45         3.19        10.82        10.65 
TCGA-06-0166 TCGA-06-0167 TCGA-06-0168 TCGA-06-0169 TCGA-06-0173 TCGA-06-0174 
        5.85        11.41        19.66         3.29         4.47         3.22 
TCGA-06-0178 TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 TCGA-06-0189 TCGA-06-0192 
       88.14        69.90        73.84        44.58        15.42        38.96 
TCGA-06-0195 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 TCGA-06-0237 
        7.40         0.53        15.02        24.16         0.72        13.64 
TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
       13.32        20.42        48.69        12.62         5.75         5.75 
TCGA-06-0648 TCGA-06-0649 TCGA-06-0650 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        9.80         2.10        23.57        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 TCGA-06-0876 
        7.86         2.70         2.70         0.92        43.46        46.19 
TCGA-06-0878 TCGA-06-0879 TCGA-06-0881 TCGA-06-0882 TCGA-06-0939 TCGA-06-1804 
        7.17        40.41        16.57        20.78        26.76        13.61 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
        1.08        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 TCGA-06-6389 
        5.95        16.64         4.37         0.43        31.50         7.79 
TCGA-06-6390 TCGA-06-6693 TCGA-06-6694 TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 
        5.39       120.56         7.36        18.02        14.73        12.99 
TCGA-12-0619 TCGA-12-0688 TCGA-12-0692 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 
       34.92        26.66         3.65        10.62         2.24        11.24 
TCGA-14-0813 TCGA-14-0817 TCGA-14-0871 TCGA-14-1043 TCGA-15-0742 TCGA-15-1444 
        1.35         5.39        28.93         0.79        13.78        50.53 
TCGA-16-0846 TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 
        3.91        31.33        14.86         5.49         1.58         7.92 
TCGA-26-6174 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        2.33         7.30         5.26        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 
        5.16        22.68        12.76         5.42        11.38         5.42 
TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        1.61        17.72        26.30 

  DDX5 MUTATED DDX5 WILD-TYPE 
           2.2            0.1 
  DDX5 MUTATED DDX5 WILD-TYPE 
         12.69         120.56 
  DDX5 MUTATED DDX5 WILD-TYPE 
         4.275         11.740 
[1] "2.2 - 12.7 (4.3)"   "0.1 - 120.6 (11.7)"
[1] "hr=" "3.6"
D36V2, continuous
D36V3, binary
                cls
clus               0   1
  DDX5 MUTATED     0   4
  DDX5 WILD-TYPE 101 175
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      0    4
  DDX5 WILD-TYPE  101  175
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  FEMALE            0            101
  MALE              4            175
[1] 2 2
[1] FALSE
D36V4, binary
                cls
clus               0   1
  DDX5 MUTATED     1   2
  DDX5 WILD-TYPE  45 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      1    2
  DDX5 WILD-TYPE   45  215
     clus
vv    DDX5 MUTATED DDX5 WILD-TYPE
  NO             1             45
  YES            2            215
[1] 2 2
[1] FALSE
D36V5, continuous
                vv
clus             GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  DDX5 MUTATED                               2                   0
  DDX5 WILD-TYPE                             9                   4
                vv
clus             UNTREATED PRIMARY (DE NOVO) GBM
  DDX5 MUTATED                                 2
  DDX5 WILD-TYPE                             263
D36V6, multiclass
                                 clus
vv                                DDX5 MUTATED DDX5 WILD-TYPE
  GLIOBLASTOMA MULTIFORME (GBM)              2              9
  TREATED PRIMARY GBM                        0              4
  UNTREATED PRIMARY (DE NOVO) GBM            2            263
[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"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX5 MUTATED       0                         0     4
  DDX5 WILD-TYPE     5                        17   248
D36V7, multiclass
                           clus
vv                          DDX5 MUTATED DDX5 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0             17
  WHITE                                4            248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
                cls
clus               0   1
  DDX5 MUTATED     0   4
  DDX5 WILD-TYPE   3 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      0    4
  DDX5 WILD-TYPE    3  218
                        clus
vv                       DDX5 MUTATED DDX5 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            4            218
[1] 2 2
[1] FALSE
